VCF file version produced by samtools0.1.6

half_programmer · 04-02-2012, 08:55 AM

Does anybody know what is the VCF version produced by samtools-0.1.6 pileup? The file produced does not have a head part, which I've checked with 'head *.vcf'.

The details in the file are like following

Y 2709606 T C T 0 4 4 0 50 0 46 1 16 0 0 0 11 0 1 30 47 15 0 0 0

Y 2709625 A C A 0 4 4 0 56 0 46 1 15 0 0 0 5 0 1 30 48 14 0 0 0

If I want to convert this type of vcf files into higher version, e.g, 4.1, is there any convenient way? Or I have to do the programming by myself?
Thanks.

nilshomer · 04-02-2012, 03:44 PM

0.1.6 is quite old, so you most likely wont get much of an answer. Is it possible to re-run with the newest version?

Richard Finney · 04-02-2012, 05:03 PM

It claims to be verion 4.1 ...

From bcftools directory for samtools-0.1.16 ...

grep VCFv *.c
vcf.c: if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
vcf.c: if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");

half_programmer · 04-02-2012, 06:14 PM

Thanks, all. Seems no easy way could do this other than self-programming. Samtools-0.1.6 was embedded in the data process pipeline, which I can't change. So fast the version was replaced by a new one.

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04-02-2012, 08:55 AM	#1
half_programmer Junior Member Location: USA Join Date: Mar 2012 Posts: 4	VCF file version produced by samtools0.1.6 Does anybody know what is the VCF version produced by samtools-0.1.6 pileup? The file produced does not have a head part, which I've checked with 'head *.vcf'. The details in the file are like following Y 2709606 T C T 0 4 4 0 50 0 46 1 16 0 0 0 11 0 1 30 47 15 0 0 0 Y 2709625 A C A 0 4 4 0 56 0 46 1 15 0 0 0 5 0 1 30 48 14 0 0 0 If I want to convert this type of vcf files into higher version, e.g, 4.1, is there any convenient way? Or I have to do the programming by myself? Thanks.

04-02-2012, 03:44 PM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	0.1.6 is quite old, so you most likely wont get much of an answer. Is it possible to re-run with the newest version?

04-02-2012, 05:03 PM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	It claims to be verion 4.1 ... From bcftools directory for samtools-0.1.16 ... grep VCFv *.c vcf.c: if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n"); vcf.c: if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");

04-02-2012, 06:14 PM	#4
half_programmer Junior Member Location: USA Join Date: Mar 2012 Posts: 4	Thanks, all. Seems no easy way could do this other than self-programming. Samtools-0.1.6 was embedded in the data process pipeline, which I can't change. So fast the version was replaced by a new one.