Hi everyone,
I've been stuck on this for several days. I want to use the samtools depth command but not only for a single bam file. I need to find a way to include all my bam files downloaded in the command.
Has anyone got an idea of how i can do this??
Thank you in advance, Maria
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written
by
Maria333 •
The usage says that you can link multiple files, make sure the specify the options before the bam files
Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
-b <bed> list of positions or regions
-f <list> list of input BAM filenames, one per line [null]
-l <int> minQLen
-q <int> base quality threshold
-Q <int> mapping quality threshold
-r <chr:from-to> region
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written
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Istvan Albert
Be warned though, samtools depth (at least as of version 1.1-30-g7f47a7c) doesn't combine the depth info across bam files for samples (same SM tag) occurring in multiple files.
I expected it to output one column per sample since most other commands work that way, but instead it outputs one column per bam file.
Hey, If my command is :
samtools depth -a -f list.txt > all.depth
and list.txt looks like this:
F1.bam
F2.bam
...
F10.bam
Is samtools output in the same order?
I mean is the third column F1.bam, the fourth F2.bam, and so on?
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