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Old 04-02-2012, 08:55 AM   #1
half_programmer
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Default 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.
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Old 04-02-2012, 03:44 PM   #2
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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?
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Old 04-02-2012, 05:03 PM   #3
Richard Finney
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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");
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Old 04-02-2012, 06:14 PM   #4
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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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