mpileup to vcf

[komalsrathi]

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:

$ samtools mpileup -u -l chr1.snps -f hg19.fa sample1_filter_sort.bam | bcftools view - > out.vcf

But this is giving me a weird output (unlike vcf):

#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

[Jetse]

Look in the samtools manual:
BCFTools view arguments:
-v Output variant sites only (force -c)

So your command becomes:

samtools mpileup -u -l chr1.snps -f hg19.fa sample1_filter_sort.bam | bcftools view -v -c - > out.vcf

EDIT:
I misunderstood your question, in my previous command you also calculate the variants...
The file you have is already a vcf file, but with all positions in it, also the positions without a SNP...