Combining gVCFs containing MNPs is not supported for Ploidy Samples
I am trying to Combine gvcfs from haplotype caller on triploid samples. I used the following command on 300 + samples (removed most to condense). I am receiving the following error: Combining gVCFs containing MNPs is not supported.
I read on an old GATK post that this was a bug that was being fixed in June 2019 but no update since.
I tried adding the -XL tag as recommended in the post, but got the exact same error. A USER ERROR has occurred: Bad input: Combining gVCFs containing MNPs is not supported. Unknown contained a MNP at A_altilis_U2-gene008.single:705
Am I not using the -XL tag correctly? How can I combine the output from haplotype caller fo triploid samples?
Code:
gatk CombineGVCFs -R /artocarpus/lauren/breadfruit/A_altilis_U2_supercontigs.fasta --variant ./gvcfs/Aa_13_Tuutou_EPoly.raw.g.vcf.gz -XL A_altilis_U2-gene008.single:705 --variant ./gvcfs/Aa_16_Puupuu_EPoly.raw.g.vcf.gz --variant ./gvcfs/Aa_17_Ulusina_WPoly.raw.g.vcf.gz --variant ./gvcfs/Aa_20160429_Micro.raw.g.vcf.gz --variant 160_Indonesia.raw.g.vcf.gz -O cohort.g.vcf.gz
Gatk version 4.1.5.0
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Looks like I need to include the ending base location of the MNP. How do I figure that out?
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Hi Lauren Audi
This is a known bug in the code and it will be fixed in the next GATK release coming in the next couple of days. You can follow the progress on this issue here: https://github.com/broadinstitute/gatk/issues/6473
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Thanks for the update. When you say the next few days...is there a specific date?
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Hi Lauren Audi
Checkout the new GATKv4.1.6.0 with this fix here: https://github.com/broadinstitute/gatk/releases/tag/4.1.6.0
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