Hello Everyone,

I used Platypus for joint variant calling using:

python Platypus.py callVariants --bamFiles=bams.list --regions=ch01 --refFile=ref.fa output=out1.vcf

I got vcf files for each chromosome and then I filtered out only SNPs using:

bcftools view --types snps out1.vcf > out1_SNP.vcf

Then I indexed the files using:

bgzip -c out1_SNP.vcf > out1_SNP.vcf.gz
tabix -p vcf out1_SNP.vcf.gz

Then I concatenate the *_SNP.vcf.gz files using bcftools concat. But I notice there are still INDELS in the file although I excluded them. For example:

CACTAATACTGT N N CACTAATACTAC TACTAATACTAC TACTAATACTAC TACTAATACTAC

I am not sure why these are still present. Can anyone please suggest any help. Thank you!