I have a vcf file with the traditional header format...
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
When reading the output, is there a simple way to scan the data (visually) and see what sites have multiple alternate alleles? I'm also seeking a simple linux tool to call the multiple alternate alleles from the vcf file. I found this one as a possibility ( how to remove multiallelic from VCF )...
awk '/#/{print;next}{if($5 !~ /,/ && length($5)==1 && length($4)==1){print}}' file.vcf
But cannot figure out the syntax error?
awk: cmd. line:1: /#/{print;next}{if($5 !~ /,/ && length($5)==1 && length($4)==1){print}}SRR1611183.gatk.vcf
awk: cmd. line:1: ^ syntax error
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written
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oars
To just output multi-allelic sites, use:
bcftools view --min-alleles 3 --max-alleles 8 MyVariants.vcf
The max alleles can be anything but, for multi-allelic sites, min alleles has to be at least 3.
If you then want to split multi-allelic calls into separate records, use:
bcftools norm -m-any MyVariants.vcf
Kevin
Thanks Kevin! This worked. Now I'm trying to understand where in the dataset I can visually see where the multi-allelic sites are located?
Edit: I think I might understand this now - looking at column 5 (ALT), those with alleles separated with a comma represent multiple alternate allele sites?
Hello friend. Yes, I was not sure what you meant by 'visually'.
I've just pulled this example from a 'random' file on my own computer:
#CHROM POS ID REF ALT
1 1581713 rs76922129 A C,G
Indeed, column #5 is ALT and is where you'll see multi-alleles being reported. In this case, the total number of alleles at this position is 3, including the ref (A, C, G).
With the bcftools norm command, this will become:
#CHROM POS ID REF ALT
1 1581713 rs76922129 A C
1 1581713 rs76922129 A G
Obviously, in a single-sample VCF for germline DNA, one must question the validity of a multi-allelic call. These are very common, however, in multi-sample VCFs and also in cancer samples, where multiple tumour clones may have been sequenced together.
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The link is dead. Can you repost it? I'd like to know how to do this using regular bash commands.
I have fixed it. Can you try again, James?