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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Support non-human variant analysis? #124

Open yige-luo opened 2 years ago

yige-luo commented 2 years ago

Dear Xiaowei,

I want to use rvtests to analyze variants data in a non-human data, whose CHROM field in the .vcf file is labeled in a different way.

 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  LC000001_14_I_LC000001_14_I     LC000001_17_F_LC000001_17_F     LC000004_01_I_LC00000
Scaffold_2      78417   Scaffold_2:78417        ATATTCATTG      A       .       .       PR      GT      0/0     0/0     0/0     0/0     0/1     0/1     0/0
Scaffold_2      80513   Scaffold_2:80513        TAAAAGAC        T       .       .       PR      GT      0/0     0/0     0/0     0/1     0/0     0/0     0/0
Scaffold_4      65529   Scaffold_4:65529        C       A       .       .       PR      GT      0/0     0/0     0/0     0/0     0/0     0/0     0/1     0/0
Scaffold_4      71567   Scaffold_4:71567        C       T       .       .       PR      GT      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0

I tried to use vcf2kinship function to get the kinship matrix, but kept encountering this error

vcf2kinship --inVcf my.vcf.gz --bn --out output

Total [ 2330000 ] VCF records ( 0 a[INFO]al/X-PATotal [ 2413517 ] VCF records have been processed. [ERROR] There are not enough variants to create kinship matrix.

I guess it may have something to do with the naming of the CHROM field, since none of my vcf records are deemed as "autosomal" by the program. I'm wondering if rvtests currently supports non-human variant analysis?

Sincerely, Yige