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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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smoove duphold error #204

Open prasundutta87 opened 1 year ago

prasundutta87 commented 1 year ago

Hi,

I am using the latest version of smoove and I am getting an error which I am unable to assess. I would be grateful if I could be helped with this. I have a trio VCF file which I have created/genotyped using sniffles2 using ONT long reads data and I want to add duphold annotations. This is the error I am getting and how do I deal with this? -

[smoove] 2022/09/27 18:40:44 starting with version 0.2.8 [smoove] 2022/09/27 18:40:44 running duphold on 3 files in 32 processes [smoove] 2022/09/27 18:44:08 [duphold] finished I, [2022-09-27T18:40:45] -- duphold: no mates found. assuming single end reads [smoove] 2022/09/27 18:44:08 [duphold] finished I, [2022-09-27T18:40:45] -- duphold: no mates found. assuming single end reads [smoove] 2022/09/27 18:44:09 [duphold] finished I, [2022-09-27T18:40:45] -- duphold: no mates found. assuming single end reads [smoove] 2022/09/27 18:44:09 starting bcftools merge [smoove] 2022/09/27 18:44:09 The REF prefixes differ: GGGGCTCCTAAGGGAATAGGTTCAGGGAGCAAGGCAGGTTTTAGGGATGGTTTAGGGAGTTCTGGGGAAATGGGGTCAATGGATGAGGCAGGTTATAGGAAGAATT vs N (106,1) Failed to merge alleles at chr1:201209820 in /tmp/tempclean-129135191/dh737826153smoove-duphold.bcf

Regards, Prasun

brentp commented 1 year ago

Hi, before running duphold on the vcf, you can run tiwih setref see here

prasundutta87 commented 1 year ago

Thanks @brentp ..I will use the tool. It also seems that the error is a deletion but the error came after many deletions later in the VCF file. Why did smoove come up with an error only on this deletion?

prasundutta87 commented 1 year ago

Just to add, the problem was solved.