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
Any help please! Best
Hi, I have same issue when conducting roh analysis, have you figure out what's going on? Thanks
Hi, any help please!
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.