make-gnotate problems

[mvelinder]

slivar_static make-gnotate *.bgz

Seems to only have processed chr10?

> slivar version: 0.1.11 5d6a5990fc06b52cbb1930806d03f786cf27d267
@["make-gnotate", "gnomad.genomes.v3.1.sites.chr10.vcf.bgz", "gnomad.genomes.v3.1.sites.chr11.vcf.bgz", "gnomad.genomes.v3.1.sites.chr12.vcf.bgz", "gnomad.genomes.v3.1.sites.chr13.vcf.bgz", "gnomad.genomes.v3.1.sites.chr14.vcf.bgz", "gnomad.genomes.v3.1.sites.chr15.vcf.bgz", "gnomad.genomes.v3.1.sites.chr16.vcf.bgz", "gnomad.genomes.v3.1.sites.chr17.vcf.bgz", "gnomad.genomes.v3.1.sites.chr18.vcf.bgz", "gnomad.genomes.v3.1.sites.chr19.vcf.bgz", "gnomad.genomes.v3.1.sites.chr1.vcf.bgz", "gnomad.genomes.v3.1.sites.chr20.vcf.bgz", "gnomad.genomes.v3.1.sites.chr21.vcf.bgz", "gnomad.genomes.v3.1.sites.chr22.vcf.bgz", "gnomad.genomes.v3.1.sites.chr2.vcf.bgz", "gnomad.genomes.v3.1.sites.chr3.vcf.bgz", "gnomad.genomes.v3.1.sites.chr4.vcf.bgz", "gnomad.genomes.v3.1.sites.chr5.vcf.bgz", "gnomad.genomes.v3.1.sites.chr6.vcf.bgz", "gnomad.genomes.v3.1.sites.chr7.vcf.bgz", "gnomad.genomes.v3.1.sites.chr8.vcf.bgz", "gnomad.genomes.v3.1.sites.chr9.vcf.bgz", "gnomad.genomes.v3.1.sites.chrX.vcf.bgz", "gnomad.genomes.v3.1.sites.chrY.vcf.bgz"]
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[W::bcf_hdr_parse] Could not parse header line: ##VEP version: v101
[W::bcf_hdr_parse] Could not parse header line: ##dbSNP version: b154
[slivar] using type float for "AF_popmax"
[slivar] 500000 variants completed. at: chr10:1561342. exact: 500000 long: 32383 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 1000000 variants completed. at: chr10:3212876. exact: 1000000 long: 56236 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 1500000 variants completed. at: chr10:4991835. exact: 1500000 long: 78152 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 2000000 variants completed. at: chr10:6746686. exact: 2000000 long: 101318 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 2500000 variants completed. at: chr10:8477147. exact: 2500000 long: 126673 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 3000000 variants completed. at: chr10:10375943. exact: 3000000 long: 145304 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 3500000 variants completed. at: chr10:12192353. exact: 3500000 long: 161556 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 4000000 variants completed. at: chr10:13892532. exact: 4000000 long: 183570 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 4500000 variants completed. at: chr10:15652512. exact: 4500000 long: 200837 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 5000000 variants completed. at: chr10:17425195. exact: 5000000 long: 217861 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 7500000 variants completed. at: chr10:26544597. exact: 7500000 long: 303415 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 10000000 variants completed. at: chr10:36006513. exact: 10000000 long: 397490 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 12500000 variants completed. at: chr10:44527747. exact: 12500000 long: 518390 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 15000000 variants completed. at: chr10:54104835. exact: 15000000 long: 592364 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 17500000 variants completed. at: chr10:63936535. exact: 17500000 long: 667922 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 20000000 variants completed. at: chr10:73629438. exact: 20000000 long: 756185 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 22500000 variants completed. at: chr10:83579588. exact: 22500000 long: 826833 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] 25000000 variants completed. at: chr10:93611355. exact: 25000000 long: 906233 in gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr10.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr11.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr12.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr13.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr14.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr15.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr16.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr17.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr18.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr19.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr1.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr20.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr21.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr22.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr2.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr3.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr4.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr5.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr6.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr7.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr8.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chr9.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chrX.vcf.bgz
[slivar] kvs.len for chr10: 35496856 after gnomad.genomes.v3.1.sites.chrY.vcf.bgz
[slivar] writing 35496856 encoded and 1307751 long values for chromosome 10
[slivar] removed 0 duplicated positions by using the value and chromosome: 10
[slivar] wrote gno.zip

[brentp]

you'll have to bcftools concat the individual chromosome files then run slivar make-gnotate on the single file.