i'm struggling to include MQ in my version 1.1 mpileup vcf output.
this used to be easy with the samtools version that i used previously.
maybe i'm missing something simple.
my whole command looks a little like this, and doesn't give MQs:
samtools mpileup -g -I -f b37.fa bam1.bam bam2.bam -l bed.bed | bcftools view
-O v -o out.vcf
including "-s" means put MQ in output, but only if you don't use bcf/vcf, so
that's no good, right? ...and indeed i get the same vcf with no MQs.
-t could be the answer, but i haven't managed to use it correctly yet.
i've tried including "-t MQ" and get this error:
Could not parse tag "MQ" in "MQ"
similarly, i tried "-t INFO" (as i'm aiming to get it into the info field of
the vcf ... clutching at straws) and got the same error.
any way to avoid these probs and make a vcf with MQ values?
thanks
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