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Old 09-26-2012, 07:35 AM   #1
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Location: UK

Join Date: Aug 2012
Posts: 7
Default Problems with outputting GT information using samtools

Hi everyone,

I'm trying to calculate heterozigosity for one individual genome using vcftools. For that, I need to have GT information in the FORMAT field for all sites. However, using the command "samtools mpileup -C50 -uDgf ref.fa output.sorted.bam | bcftools view -cg - > output.vcf" in samtools, only adds the GT information for variable sites relative to the reference, which is apparently a problem for vcftools. Anyone has any idea how to tell samtools to include the GT field for all sites? I thought the -g option in both mpilup and bcfview would take care of it, but apparently not.

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