Open splaisan opened 6 years ago
Dear, I ran varscan mpileup2cns (v2.4.3) on some data and when analysing the vcf with bcftools stats got an error
$ bcftools stats --fasta-ref Ref.fasta variants.vcf.gz > vcf.stats Sanity check failed, the reference sequence differs: NC_030973.1:129900+2 .. G vs Y samtools faidx R64_SEUB3.0_merged.fasta NC_030973.1:129900-129902
After inspecting this closely (https://github.com/samtools/bcftools/issues/691#issuecomment-337218492) @pd3 came to the conclusion that varscan is not handling IUPAC ref bases as it should and should have made CAC out of the reference CAY bases instead of the returned CAG.
Could you please confirm and maybe fix this IUPAC replacement case for the ref field? Thanks in advance
## reference info samtools faidx R64_SEUB3.0_merged.fasta NC_030973.1:129900-129902 NC_030973.1:129900-129902 CAY $ tabix variants.vcf.gz NC_030973.1:129900-129902 NC_030973.1 129900 . CAG C . PASS ADP=22;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:49:33:22:10:13:48.15%:1.1242E-5:23:12:6:4:3:10
Dear, I ran varscan mpileup2cns (v2.4.3) on some data and when analysing the vcf with bcftools stats got an error
After inspecting this closely (https://github.com/samtools/bcftools/issues/691#issuecomment-337218492) @pd3 came to the conclusion that varscan is not handling IUPAC ref bases as it should and should have made CAC out of the reference CAY bases instead of the returned CAG.
Could you please confirm and maybe fix this IUPAC replacement case for the ref field? Thanks in advance