Error parsing Exome Sequencing Project (ESP) VCF using vcf_melt #92

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cboustred opened this Issue Feb 5, 2013 · 3 comments

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@cboustred

Hi James,

I believe I'm using the latest PyVCF version (PyVCF-0.6.3)

I'd like to flatten the ESP VCFs into tab delimited files. The VCFs can be downloaded from here (http://evs.gs.washington.edu/evs_bulk_data/ESP6500SI.snps_indels.vcf.tar.gz)

I have unzipped them and tried running

vcf_melt ESP6500SI.chr1.snps_indels.vcf

And get the following output

SAMPLE FILTER CHROM POS REF ALT ID info.DBSNP info.EA_AC info.AA_AC info.TAC info.MAF info.GTS info.EA_GTC info.AA_GTC info.GTC info.DP info.FG info.GM info.AA info.AAC info.PP info.CDP info.PH info.CP info.CG info.GL info.GS info.CA info.EXOME_CHIP info.GWAS_PUBMED
Traceback (most recent call last):
File "./vcf_melt", line 40, in
for sample in record.samples:
TypeError: 'NoneType' object is not iterable

Any advice on how I can fix this would be much appreciated

Thanks

Chris

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jamescasbon Feb 5, 2013

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Chris, VCF melt keeps on failing you!

I'll check it out.

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jamescasbon commented Feb 5, 2013

Chris, VCF melt keeps on failing you!

I'll check it out.

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jamescasbon Jul 15, 2013

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Is this still a problem?

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jamescasbon commented Jul 15, 2013

Is this still a problem?

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jamescasbon Dec 3, 2013

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Closing, no response from poster.

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jamescasbon commented Dec 3, 2013

Closing, no response from poster.

@jamescasbon jamescasbon closed this Dec 3, 2013

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