bcftools roh with -e option... never finish
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2.7 years ago
emmanouil.a ▴ 110

Hi,

I have 25 vcf with only GT values, and I merged them with "vcf-merge \${all_samples}"

after merge I have some situations like the following where not all samples have a GT... in general is normal ...

CHROM   POS   ID   REF   ALT   QUAL   FILTER   INFO   FORMAT   wes001   wes002   wes003   ...   wes025

chr1    12807   .   C   T   39.94   .   AC=3;AN=4;SF=19,24  GT  .   .   .   .   .   .   .   .   .   .   .   .   .   .   ..  .   .   .   1/1 .   .   .   .   0/1


1) when I run bcftools roh with this code everything seems ok

bcftools roh -G30 merged.vcf.gz -o roh_merged.vcf.gz.txt"


With this code the number of roh in each sample are less here than when I run bcftools roh in eah sample separately, why? because I use "--AF-dflt 0.4"?

code for roh calling in each sample sepraterlly

bcftools roh -G30 --AF-dflt 0.4 "single_sample.vcf.gz


2) when I use this code, to calculate and use the AF on fly ...

 bcftools roh -G30 -e sample.list merged.vcf.gz -o roh_merged.vcf.gz.txt"


the command run without any result and after one hour it freeze!

The only log that I have are these:

Number of target samples: 25
Number of --estimate-AF samples: 25
Number of sites in the buffer/overlap: unlimited


sample.list are the sample names reported in the vcf (wes001, wes002) and here like a column, one name in each line...

 -e, --estimate-AF [TAG],<file>
estimate AF from FORMAT/TAG (GT or PL) of all samples ("-") or samples listed in <file>. If TAG is not given, the frequency is estimated from GT by default


bcftools roh • 958 views
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Hi, I have same issue when conducting roh analysis, have you figure out what's going on? Thanks

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I have the same issue with RAD-seq data. I think it is related to the distribution of the genotype data across chromosomes. Perhaps, the software has difficulties to reach convergence when it has to estimate some parameters. I have posted a similar question in the github of bcftools, hoping to get an answer.