Dear all,
[I sent the following message to samtools-help mailling list, but no luck. Therefore, I post it here. I am sorry for sending the message twice.]
I tried to use samtools version 0.1.8 and version 0.1.16 to generate .plp files on the same bam file:
samtools.0.1.8 pileup -f genome_hg19.fa -c accepted_hits.sorted.bam > normal.raw.plp
samtools.0.1.16 pileup -f genome_hg19.fa -c accepted_hits.sorted.bam > normal.raw.plp
However, I found that the plp file generated by 0.1.16 version is several times bigger than the plp file compiled by 0.1.8 version of samtools.
I tried -B option to disable BAQ, but the result is still the same. I checked the coverage on the genome of the two plp files, and I found they have huge difference.
What happened? I googled the question and found someone has ever asked the same question recently:
It seemed like not just me suffering this problem.
Could someone please help me explain the problem? Thanks!
Bests,
Woody
[I sent the following message to samtools-help mailling list, but no luck. Therefore, I post it here. I am sorry for sending the message twice.]
I tried to use samtools version 0.1.8 and version 0.1.16 to generate .plp files on the same bam file:
samtools.0.1.8 pileup -f genome_hg19.fa -c accepted_hits.sorted.bam > normal.raw.plp
samtools.0.1.16 pileup -f genome_hg19.fa -c accepted_hits.sorted.bam > normal.raw.plp
However, I found that the plp file generated by 0.1.16 version is several times bigger than the plp file compiled by 0.1.8 version of samtools.
I tried -B option to disable BAQ, but the result is still the same. I checked the coverage on the genome of the two plp files, and I found they have huge difference.
What happened? I googled the question and found someone has ever asked the same question recently:
It seemed like not just me suffering this problem.
Could someone please help me explain the problem? Thanks!
Bests,
Woody
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