Entering edit mode
2.8 years ago
Siddharth
•
0
I'm using the gatk4 standard pipeline to create .bams from paired end fastqs using cutadapt and bwa 0.7.16 to hs37d5. The pipeline runs without errors and I get .bams of the expected size. However, when I view them in igv hg19 they look like this, everywhere:
Has anyone seen this before? What do you suggest?
Are you aligning to the right genome (and build)?
hs37d5 is correct as far as I know. I am checking with the sequencer to be sure. Even if the genome build is not right, would almost EVERY position appear heterozygous?