# Invalid genotype signature error on LoadVCF

**URL:** <https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951>\
**Category:** Hail Query & hailctl\
**Created:** [May 7, 2019, 3:18pm UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951 "2019-05-07T15:18:55Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![marcusbb](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@marcusbb](https://discuss.hail.is/u/marcusbb)\
**Post date:** [May 7, 2019, 3:18pm UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951/1 "2019-05-07T15:18:55Z")

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When Loading and aggregate VCF built with Illumina agg software from Strelka called Illumina gVCFs, via:

var\_mt = hl.import\_vcf(in\_files, force\_bgz=True)

we get the following error:

HailException: invalid genotype signature: expected signatures to be identical for all inputs.  
s3://regap-183760095058-eu-west-2-data/private-preview/subset\_10\_22/20k\_GRCH38\_germlinechr20\_13754086\_18515298.vcf.bgz: struct{GT: call, DP: int32, DPF: int32, AD: array, GQ: int32, PF: array}  
s3://regap-183760095058-eu-west-2-data/private-preview/subset\_10\_22/20k\_GRCH38\_germlinechr20\_61920330\_64334162.vcf.bgz: struct{GT: call, DP: int32, DPF: int32, AD: array, GQ: int32, PF: array, PL: array}

Is there a restriction on one, or more, or a combination of attributes that we need to follow.

Thanks

Mark

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [May 7, 2019, 6:05pm UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951/2 "2019-05-07T18:05:29Z")

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These are both valid VCFs to Hail if you import them individually, but Hail rejects importing multiple VCFs with the same `import_vcf`invocation if their schemas differ. That’s what’s going on here – one of the vcfs has a PL, one doesn’t.

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [May 7, 2019, 6:07pm UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951/3 "2019-05-07T18:07:11Z")

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I should also note that Hail doesn’t do nicely with gVCFs right now. One of our team members is working on a gVCF import/merging algorithm and sparse genotytpe matrix representation, though, which we expect to be usable and documented in a couple of months.

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**Author:** ![marcusbb](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@marcusbb](https://discuss.hail.is/u/marcusbb)\
**Post date:** [May 8, 2019, 10:11am UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951/4 "2019-05-08T10:11:48Z")

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Excellent. Thanks for the clarification

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [May 8, 2019, 10:24am UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951/5 "2019-05-08T10:24:31Z")

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also note that `import_vcf` supports a list of files with the _same samples_ and non-overlapping genomic intervals. It doesn’t support importing multiple single-sample [g]VCFs.

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**Author:** ![marcusbb](https://avatars.discourse-cdn.com/v4/letter/m/8491ac/32.png) [@marcusbb](https://discuss.hail.is/u/marcusbb)\
**Post date:** [May 15, 2019, 2:39pm UTC](https://discuss.hail.is/t/invalid-genotype-signature-error-on-loadvcf/951/6 "2019-05-15T14:39:25Z")

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Well. We’re running against 20K aggregate gVCF , but look forward to the update 😉