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SHAPEIT4 incorrect number of columns

Hello, I hope that this is not too basic a question.

I am trying to phase a dataset in SHAPEITv4. QC was done in plink by a colleague, and I converted it to .vcf format, compressed it and produced the necessary index file for SHAPEITv4 to read.

I am getting an error at the VCF parsing stage:

ERROR: Parsing line 0 : incorrect number of columns, observed: 1 expected: 3

I am not certain where it is expecting to see three columns. The .vcf header should have one, and the body at least eight. There is obviously something that I am not aware of, and I would be very grateful for any pointers.

Thanks,

Mike

software error
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updated by readingandrelaxing • readingandrelaxing • written by michael.turner • michael.turner

How did you convert it to .vcf and the bgz format?

also, can you post a sample of the header and the first non-header line of the .vcf?

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written by 4galaxy77 4galaxy77

Hi there,

Sorry, I have just seen this. I converted to vcf in plink:

plink --bfile my_bfile --recode vcf --out my_vcf_file

I subsequently compressed it using bgzip:

bgzip -c my_vcf_file.vcf > my_vcf_file.vcf.gz

Header sample:

'##fileformat=VCFv4.3'

'##fileDate=20210114'

'##source=PLINKv2.00'

'##contig=<id=1,length=248928329'< p="">

The first non-header line contains a column for each individual, so is too long to post, but the first eight columns with two sample rows are:

'#CHROM POS ID REF ALT QUAL FILTER INFO'

1 792461 GSA-rs116587930 G A . . PR

1 817341 rs3131972 G A . . PR

Many thanks,

Mike

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written by michael.turner • michael.turner

Hi michael, I have the same error. Were you able to fix this?

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written by Beatriz • Beatriz

I've run into the same problem. Any chance you figured out what was wrong?

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written by prmshakya • prmshakya

I had this issue except it said there were 4 columns instead of 3. I thought at first there was something wrong with either my input or reference vcd, but it turns out my map file had an extra column, so check that if you get this issue.

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written by readingandrelaxing • readingandrelaxing

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