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?
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 220.127.116.11
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