Entering edit mode
4.9 years ago
evelyn
▴
230
I am using GATK
for variant calling. It works and give results but the number of SNPs found is significantly very low as compared to samtools
. Is this fine or there is an error?
I understand there will be difference in the number of SNPs but the vcf file size by gatk is 10,000 times less than the vcf file size by samtools. Is this large difference normal?
File size is not an indicator in most cases, but 10,000 times smaller does sound a little suspect. Can you check the GATK logs and ensure it ran to completion?
Yes, it ran to completion and didn't give any error.
Just to be sure, they're both the same format, correct? Variants can be in VCF/BCF formats and either of those formats can be compressed/uncompressed. Does running
htsfile <filename>
give the same output on both? Plus, the one from GATK is not a gVCF file, correct?If you could give us the exact commands you used, that would help a lot.
I am using this code to call SNPs for DNA seq paired end files aligned using
bowtie2
:Using
GATK
:Using
samtools
: