DAY-EC activated.
DAY-EC activated.
want=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHCv5q
total 130K
drwxr-xr-x  4 root root 33K May 29 02:51 .
drwxr-xr-x  4 root root 33K May 29 02:51 ..
drwxr-xr-x 10 root root 33K May 29 02:51 v4.2.1
drwxr-xr-x  3 root root 33K May 26 08:14 v5.0q
total 328K
drwxr-xr-x 10 root root  33K May 29 02:51 .
drwxr-xr-x  4 root root  33K May 29 02:51 ..
drwxr-xr-x 11 root root  33K May 29 02:51 HG001
drwxr-xr-x 12 root root  33K May 26 08:14 HG002
drwxr-xr-x  8 root root  33K May 29 02:51 HG003
drwxr-xr-x 11 root root  33K May 29 02:51 HG004
drwxr-xr-x 11 root root  33K May 29 02:51 HG005
drwxr-xr-x 13 root root  33K May 29 02:51 HG006
drwxr-xr-x 11 root root  33K May 29 02:51 HG007
drwxr-xr-x  3 root root  33K May 29 02:51 HG2
-rwxr-xr-x  1 root root    0 May 26 07:52 bed_regions.log
-rwxr-xr-x  1 root root  642 May 26 07:52 calc_uniq_footprint.py
-rwxr-xr-x  1 root root  636 May 26 07:52 calc_uniq_footprint.py~
-rwxr-xr-x  1 root root 1.5K May 26 07:52 create_clinv.sh
-rwxr-xr-x  1 root root  716 May 26 07:52 create_clinv.sh~
-rwxr-xr-x  1 root root  746 May 26 07:52 proc_regions.sh
total 390K
drwxr-xr-x 12 root root 33K May 26 08:14 .
drwxr-xr-x 10 root root 33K May 29 02:51 ..
drwxr-xr-x  2 root root 33K May 29 02:51 altair-v1.1
drwxr-xr-x  2 root root 33K May 29 02:51 clinvar_genes
drwxr-xr-x  3 root root 33K May 29 02:51 giabHC
drwxr-xr-x  2 root root 33K May 29 02:51 giabHC_x_clinvar_genes
drwxr-xr-x  2 root root 33K May 29 02:51 giabHC_x_ultima
drwxr-xr-x  2 root root 33K May 29 02:51 giabHC_x_ultima_x_clinvar
drwxr-xr-x  2 root root 33K May 29 02:51 giabHCv5q
drwxr-xr-x  2 root root 33K May 29 02:51 hg38
drwxr-xr-x  2 root root 33K May 29 02:51 hg38_m_giabHC
drwxr-xr-x  2 root root 33K May 29 02:51 ultima
total 103K
drwxr-xr-x  2 root root 33K May 29 02:51 .
drwxr-xr-x 12 root root 33K May 26 08:14 ..
lrwxrwxrwx  1 root root 137 May 26 07:49 HG002.bed -> /fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.benchmark.bed
lrwxrwxrwx  1 root root 130 May 26 07:49 HG002.vcf.gz -> /fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.vcf.gz
lrwxrwxrwx  1 root root 134 May 26 07:49 HG002.vcf.gz.tbi -> /fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.vcf.gz.tbi

HG002 candidate files under giab snv:
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/altair-v1.1/HG002.bed	5475200
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/altair-v1.1/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/altair-v1.1/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/clinvar_genes/HG002.bed	4684427
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/clinvar_genes/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/clinvar_genes/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/clinvar_genes/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/clinvar_genes/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/clinvar_genes/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/HG002.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_all.vcf.gz	249469064
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_all.vcf.gz.tbi	1801590
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_annotated.vcf.gz	1611292710
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_annotated.vcf.gz.tbi	2115301
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_benchmark_hifiasm_v11_phasetransfer.vcf.gz	175186444
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_benchmark_hifiasm_v11_phasetransfer.vcf.gz.tbi	1633465
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_benchmark_phased_MHCassembly_StrandSeqANDTrio.vcf.gz	162490215
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_benchmark_phased_MHCassembly_StrandSeqANDTrio.vcf.gz.tbi	1661777
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_callablemultinter_gt0.bed	9568083
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_GRCh38_1_22_v4.2.1_filteredsites.bed	54218978
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_NA24385_GRCh38_1_22_v4.2_benchmark_phased_StrandSeq_whatshap.vcf.gz	158066596
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/HG002_NA24385_GRCh38_1_22_v4.2_benchmark_phased_StrandSeq_whatshap.vcf.gz.tbi	1657761
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_10xGenomics.vcf.gz	1584635531
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_10xGenomics.vcf.gz.tbi	2069463
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_10xGenomics_callable.bed	18521699
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_PacBio_HiFi_DeepVariant.vcf.gz	112224382
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_PacBio_HiFi_DeepVariant.vcf.gz.tbi	1606512
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_PacBio_HiFi_DeepVariant_callable.bed	2933079
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_PacBio_HiFi_GATK4.vcf.gz	250604472
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_PacBio_HiFi_GATK4.vcf.gz.tbi	1565969
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC/SupplementaryFiles/inputvcfsandbeds/HG002_GRCh38_1_22_PacBio_HiFi_GATK4_callable.bed	68757
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_clinvar_genes/HG002.bed	5658414
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_clinvar_genes/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_clinvar_genes/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_clinvar_genes/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_clinvar_genes/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_clinvar_genes/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002.bed	171587412
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima_x_clinvar/HG002.bed	39085649
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima_x_clinvar/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima_x_clinvar/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima_x_clinvar/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima_x_clinvar/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima_x_clinvar/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38/HG002.bed	426
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002.bed	11597738
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/ultima/HG002.bed	239624499
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/ultima/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/ultima/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/ultima/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/ultima/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/ultima/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed	11494021
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/clinvar_genes/HG002.bed	4684427
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/clinvar_genes/HG002.vcf.gz	156252944
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/clinvar_genes/HG002.vcf.gz.tbi	1657747
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.benchmark.bed	685544
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.vcf.gz	42067644
/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.vcf.gz.tbi	1547524

giabHCv5q paths:
d	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHCv5q	33280
d	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q	33280
f	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.benchmark.bed	685544
f	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.vcf.gz	42067644
f	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002_GRCh38_v5.0q_smvar.vcf.gz.tbi	1547524
l	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHCv5q/HG002.bed	137
l	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHCv5q/HG002.vcf.gz	130
l	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHCv5q/HG002.vcf.gz.tbi	134
l	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002.bed	137
l	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002.vcf.gz	130
l	/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v5.0q/HG002/giabHCv5q/HG002.vcf.gz.tbi	134
