Hi everyone,
I know there is a perl script 'sam2vcf.pl' to convert a pileup file to .vcf format. But I wanted to know whether there is any tools/script that converts mpileup format to .vcf format WITHOUT calling variants. I used:
But this is giving me a weird output (unlike vcf):
I know there is a perl script 'sam2vcf.pl' to convert a pileup file to .vcf format. But I wanted to know whether there is any tools/script that converts mpileup format to .vcf format WITHOUT calling variants. I used:
$ samtools mpileup -u -l chr1.snps -f hg19.fa sample1_filter_sort.bam | bcftools view - > out.vcf
HTML Code:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT P01273_DCM chr1 1211292 . C X 0 . DP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0.000000,0.000000,0.000000,0.000000 PL 0,0,0 chr1 2069172 . C X 0 . DP=0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0.000000,0.000000,0.000000,0.000000 PL 0,0,0
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