N in VCF for mpileup #13
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@ulfschaefer suggested we properly fix the "./." record with appropriate reference pulled out from reference file provided. |
alexjironkin
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Jun 9, 2016
mpileup doesn't output all data, so we had to add a fudge to insert ./. record in the missing positions. Before we added N as reference base, however, if reference is provided then appropriate reference base is added.
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For mpileup we have to insert bases because mpileup removes records with no coverage.
The -a option in mpileup is not working currently that allows to emit all sites (even with no coverage). Instead we insert ./. record where that is detected with 'N' as reference. However, N in reference causes problems in vcf2fasta because we make sure reference is the same for all records. And there are instances when this happens:
vcf1:
chr1 12672 . N . . mq_score:30;mq0_ratio:0.1;min_depth:10;dp4_ratio:0.9 . GT ./.vcf2:
When the reference is checked, you get ['N', 'T'] which doesn't match up, so vcf2fasta errors thinking something went wrong.
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