Less than 10,000 variants (0 detected variants) with AD (or AO) and DP available

[wangDanHua1]

bash /data/software_wdh/AutoMap-master/AutoMap_v1.2.sh --vcf /data/software_wdh/AutoMap-master/Test/TestSample.vcf --out /data/software_wdh/AutoMap-master/test/ --genome hg19

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. grep: this version of PCRE is compiled without UTF support

WARNING: No sample name provided through --id option, name will be taken from the VCF: TestSample

ERROR: Less than 10,000 variants (0 detected variants) with AD (or AO) and DP available. Exit.

[wangDanHua1]

grep -P changed grep -E

[mquinodo]

Hello, Was the problem solved changing grep -P to grep -E?

[anjalijain22]

Hello, I also encountered this issue and figured it was because my input was a bgzipped file (.gz). After providing an unzipped VCF, I was able to run AutoMap without any issues. Putting this here for future users in case anyone else is facing this error.