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mquinodo / AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.
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## ERROR: Less than 10,000 variants (0 detected variants) with AD and DP available. Exit. #4

Closed mvheetve closed 3 years ago

mvheetve commented 3 years ago

Hi,

I got the following error when analyzing one of my files:

bash /kyukon/data/gent/vo/000/gvo00082/research/mvheetve/temp/CEP162/AutoMap/AutoMap_v1.0.sh --vcf /kyukon/data/gent/vo/000/gvo00082/research/mvheetve/temp/CEP162/fastq/analysis/samples_D1800416-merged/final/18-00416/18-00416-gatk-haplotype_norm_nonref.vcf.gz --genome hg38 --out /kyukon/data/gent/vo/000/gvo00082/research/mvheetve/temp/CEP162/common_reanalysis
# bcftools higher or equal to v1.9
# bedtools higher or equal to v2.24.0
# perl higher or equal to v5.22.0
# R higher or equal to v3.2.0
## Parameters used by default:
 -> No use of --DP option, value set as default: 8
 -> No use of --binomial option, value set as default: 0.000001
 -> No use of --percaltlow option, value set as default: 0.25
 -> No use of --percalthigh option, value set as default: 0.75
 -> No use of --window option, value set as default: 7
 -> No use of --windowthres option, value set as default: 5
 -> No use of --minsize option, value set as default: 1
 -> No use of --minvar option, value set as default: 25
 -> No use of --minperc option, value set as default: 88
 -> No use of --maxgap option, value set as default: 10
 -> chrX will NOT be included in the analysis and in the graphics.
 -> Homozygosity regions will be extended to nearest variant with maximum of 1 Mb.
## WARNING: No sample name provided through --id option, name will be taken from the VCF: 18-00416
## ERROR: Less than 10,000 variants (0 detected variants) with AD and DP available. Exit.

I tried setting --DP to 0, but same error occured. vcf file attached and output of bcftools query for FORMAT/AD and FORMAT/DP, which clearly shows AD and DP values for all variants (albeit in the low numbers at times). Any idea what might be the problem?

Regards mvheetve

mvheetve commented 3 years ago

Nevermind, just noticed vcf was still gzipped. Would be nice to add .gz functionality in the future though.

Regards mvheetve