Dear all,
I need help with allele information from samtools mpileup contents
I have the following workflow for diagnostics:
samtools view -b whole_exome.sorted.bam chr2:12345678-32345678 > zoom_region.bam
samtools mpileup -f ref.fa -B -q 1 -Q 30 -SD zoom_region.bam > info.mpileup.txt
The subsequent info.mpileup.txt has information as described in
Is there a script or automated method that can parse the allele info: #A, T, G, C .. from the mpileup / pileup information of the original bam file. I need to repeat this for many base positions, hence the need to automate it. Hope you can please help. Would appreciate any help / pointers.
Thanks in advance,
Best,
sarosh
I need help with allele information from samtools mpileup contents
I have the following workflow for diagnostics:
samtools view -b whole_exome.sorted.bam chr2:12345678-32345678 > zoom_region.bam
samtools mpileup -f ref.fa -B -q 1 -Q 30 -SD zoom_region.bam > info.mpileup.txt
The subsequent info.mpileup.txt has information as described in
Is there a script or automated method that can parse the allele info: #A, T, G, C .. from the mpileup / pileup information of the original bam file. I need to repeat this for many base positions, hence the need to automate it. Hope you can please help. Would appreciate any help / pointers.
Thanks in advance,
Best,
sarosh
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