Hi Anton,
I personally use Picard's MarkDuplicates for this. With METRIC_FILE option it
reports everything in an output file for you.
Cheers,
Chris
On 02/03/2017, 11:13, "Anton Kratz"
<anton.kr...@riken.jp<mailto:anton.kr...@riken.jp>> wrote:
Is there a way how I can figure out how many reads have been removed by
applying rmdup?
I have a file foobar.bam containing paired-end reads, and I want to remove PCR
duplicates, and also I want to know how many pairs have been removed. Here is
what I am doing at the moment:
# sort foobar.bam
samtools sort -n foobar.bam -o foobar.srtd.bam
# apply fixmate
samtools fixmate foobar.srtd.bam foobar.srtd.matefixed.bam
# do the PCR duplicate removal
samtools rmdup foobar.srtd.matefixed.bam foobar.rmdupped.bam
# make sure that the output is sorted
samtools sort -n foobar.rmdupped.bam -o foobar.rmdupped.srtd.bam
What I am doing then is to run samtools stat on foobar.srtd.matefixed.bam (file
before the rmdup stage) and foobar.rmdupped.bam (file after the rmdup stage).
Then I could write a script that parses the relevant numbers out of the output.
Is this the way to it? Is there a more straightforward way?
I need to programmatically access for a bam file how many PCR duplicates have
been removed with rmdup. Or, I need this as a parseable output from the
samtools rmdup command.
Thanks,
Anton
## Versions used:
samtools --version samtools 1.3.1
Using htslib 1.3.1
The University of Dundee is a registered Scottish Charity, No: SC015096
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
