I'm trying to call SNPs from an alignment (BWA) to a reference genome using bcftools (0.1.18). However, my output contains INDELs too. I'm looking for _just_ the SNPs. Here's what I've done:
samtools mpileup -uf reference.fasta output.bam | bcftools view -bvcg - > variants.bcf bcftools view variants.bcf | vcfutils.pl varFilter > filtered_variants.vcf
And the output looks like this:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT WGS
Chrom1 4 . C T 125 . DP=37;VDB=0.0026;AF1=1;AC1=2;DP4=0,0,35,2;MQ=59;FQ=-138 GT:PL:GQ 1/1:158,111,0:99
Chrom1 19 . CAAAAAAAAAAAA CAAAAAAAAAA,CAAAAAAAAA 145 . INDEL;DP=162;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,65,76;MQ=55;FQ=-290 G
I want a vcf with just the SNPs i.e. the ones like Chrom1 position 4, not the INDELs. There isn't an 'INDEL' column, so can't just remove that column.......I'm clearly missing something! Ideas would be greatly appreciated.