Hi, I'm using The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34
I was running the UnifiedGenotyper tools on a 100bp paired end read with the the command below:
Program Args: -T UnifiedGenotyper -R ref.fasta -I realignedBwa.bam -glm BOTH -log variantsCalling.log -o bwa_variants.vcf
I noticed that only SNPs were called and not a single indel was called. however, when i used a 150bp paired end read with the similar command above it worked fine, the SNPs and Indels were called.
To make sure that the realignedBWA.bam file that i used was not corrupt/malformed, i used two different other pileup program on this bam file and the SNPs and Indels were called nicely. Hope you can take a look at this. I attached together the log file just in case
thanks in advance