Closed Saranya-Balachandran closed 5 years ago
Saranya-Balachandran
commented
5 years ago On running on the test data generated by make test in human_trio receiving the same error dng dnm auto --ped human_trio/ped/trio.ped --vcf human_trio/bcftools/trio.call.vcf
reedacartwright
commented
5 years ago The sample data you used is for dng call so the error is expected.
It appears you are using the wrong pedigree format for dng dnm. Can you update to the format sorted by dng dnm?
On Thu, Jul 18, 2019, 07:54 Saranya-Balachandran notifications@github.com wrote:
On running on the test data generated by make test in human_trio receiving the same error dng dnm auto --ped human_trio/ped/trio.ped --vcf human_trio/bcftools/trio.call.vcf
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Saranya-Balachandran
commented
5 years ago Please find below my ped format
SID93046 . . 2 = SID93044 . . 1 = SID93041 SID93044 SID93046 1 =
reedacartwright
commented
5 years ago That's the format recognized by dng-call. To use dng-dnm follow the instructions here:
https://github.com/ultimatesource/denovogear/blob/develop/README.md#about-sampleped
On Thu, Jul 18, 2019, 09:43 Saranya-Balachandran notifications@github.com wrote:
Please find below my ped format
PEDNG v1.0
ID Dad Mom Sex Samples
SID93046 . . 2 = SID93044 . . 1 = SID93041 SID93044 SID93046 1 =
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Saranya-Balachandran
commented
5 years ago Thank you!
Hi, On running dng dnm auto --vcf vcf_f --ped ped_f -w out.vcf, I get [E::bcf_hdr_add_sample] Duplicated sample name '.' Aborted (core dumped) On querying the sample names using bcftools I get three distinct sample names. The bcf file has DP, PL record for each sample individually.
Kindly help in understanding this issue. I'm runing in the denovogear developer mode
Regards, Saranya