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bcftools multiallelic split not working

I am attempting to split multiallelic sites using bcftools norm with the following command:

zcat ${inputVcf} | \
sed 's/AD,Number=./AD,Number=R/g' | \
sed 's/ADR,Number=./ADR,Number=R/g' | \
sed 's/ADF,Number=./ADF,Number=R/g' | \
bcftools norm \
  --fasta-ref ${genomeFa} \
  --check-ref s \
  --multiallelics -any \
  --output ${outputVcf}

The sed commands were based on the recommendation from here. However I'm still getting FORMAT entries such as the following: GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL 1/0:44:44:56:1,10,5:1,4,2:0,6,3:PASS:511,99,48 ./.:.:.:.:.:.:.:.:. 0/1:53:53:63:0,12,6:0,4,1:0,8,5:PASS:483,210,164 which are clearly multiallelic. Anybody know how to fix this?

bcftools vcf
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updated by Ram Ram • written by from the mountains from the mountains

1 answer

Hi, I think that you misinterpret what is a 'multi-allelic' call. The entry that you posted is not multi-allelic in this sense. A multi-allelic call may look like:

A      G,T    1/2

Thus, the genotype is GT. After splitting, this would become:

A      G      0/1
A      T      0/1

Kevin

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written by Kevin Blighe Kevin Blighe

i think that clarifies things and pointed me in the right direction. what happened was, the vcf file was normalized in a previous step so the ALT column was split, but fields like AD remained as they were because those fields were was ignored, and their data types were still wrong. fixing the upstream implementation of bcftools norm worked for me and now both my ALT and AD fields are split as i expect them.

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written by from the mountains from the mountains

How can i achieve that you discribed above for a VCF file ?

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written by summerday1112 • summerday1112

I had a vcf file only contains snp variants (bi and multi) after GATK VQSR , now I want to split multiallelic variant into biallelic variant, the order I used is : bcftools norm -m -snps snp.2.vcf.gz -Ov -o output then it throw an error: Error: wrong number of fields in INFO/MLEAC at 2:10443, expected 2, found 1 how can i solve it?

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written by summerday1112 • summerday1112

first perform bcftools norm -m-any then VQSR

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written by DareDevil DareDevil

an off topic question: is there a mention of bcftool norm in any publication?

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written by Bioinformatics_NewComer Bioinformatics_NewComer

You will not be able to find bcftools norm in any publication. But you will be able to find bcftools in publications

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updated by Ram Ram • written by DareDevil DareDevil

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