Entering edit mode
4.4 years ago
evelyn
▴
220
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!