Hi all!!
I am new in this forum, I am working on Illumina NGS data since recently, and I have some troubles!
I was using this command:
samtools mpileup -C50 -q 25 -f reference.fa file.bam > file.mpileup
when I realised it was producing strange valleys in base quality phred scores in correspondence to mismatches to the reference genome, I now think the BAQ (base alignment quality computation) was responsible for those, so I added the -B option:
samtools mpileup -B -C50 -q 25 -f reference.fa file.bam > file.mpileup
Now the valleys in base quality seem to have disappeared, but I see much lower coverage in different regions of the genome… Of course, the 2 commands were used on the very same .bam file, nothing else should be different apart from the -B option…
I can't see how the -B option can cause the discard of any read, thus the lower coverage I see in my pileup files. Unless in the previous command, the default BAQ computation was disabling some other option, like the -q 25???
Any help is veeeeery welcome!!
Thanks a lot!
grillino
I am new in this forum, I am working on Illumina NGS data since recently, and I have some troubles!
I was using this command:
samtools mpileup -C50 -q 25 -f reference.fa file.bam > file.mpileup
when I realised it was producing strange valleys in base quality phred scores in correspondence to mismatches to the reference genome, I now think the BAQ (base alignment quality computation) was responsible for those, so I added the -B option:
samtools mpileup -B -C50 -q 25 -f reference.fa file.bam > file.mpileup
Now the valleys in base quality seem to have disappeared, but I see much lower coverage in different regions of the genome… Of course, the 2 commands were used on the very same .bam file, nothing else should be different apart from the -B option…
I can't see how the -B option can cause the discard of any read, thus the lower coverage I see in my pileup files. Unless in the previous command, the default BAQ computation was disabling some other option, like the -q 25???
Any help is veeeeery welcome!!
Thanks a lot!
grillino
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