small .bam files to test GATK Variant Discovery pipeline
0
0
Entering edit mode
4.1 years ago
alongalor • 0

Could someone refer me to where I could download the smallest possible .bam files to test my GATK Best Practices Variant Discovery pipeline? My pipeline uses the -L option to parallelize over different chromosomes - I would like to test this functionality and so I would like a full .bam file that has data from all chromosomes and will not cause GATK to crash.

Thanks a lot!

bam small GATK test Variant Discovery • 1.7k views
ADD COMMENT
0
Entering edit mode

Just use any BAM that you have on disk, make a little BED file with one interval per chromosome, e.g. chr1-22 from 6000000-6100000 respectively, and use SAMtools view to get a subset of the whole BAM:

samtools view -bh -o out_subset.bam input.bam -L regions.bed

That should be sufficient for testing purposes.

ADD REPLY
0
Entering edit mode

This worked perfectly in terms of splitting the bam file but it caused GATK to crash with a strange error... my pipeline of course still works with the original bam file before it was split.

ADD REPLY

Login before adding your answer.

Traffic: 2022 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6