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twolinin / longphase

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is it possible to parse SNP call sets produced other than deepvariant? #4

Closed yekaizhou closed 2 years ago

yekaizhou commented 2 years ago

it seems longphase will treat unphased longshot output vcf files as already phased, and will not proceed further.

twolinin commented 2 years ago

it seems longphase will treat unphased longshot output vcf files as already phased, and will not proceed further.

Hi yekaizhou, It is allowed to re-phase a VCF now. Please clone the latest version.

yekaizhou commented 2 years ago

Hi, this time longshot results can be accepted, but raised error terminate called after throwing an instance of 'std::invalid_argument'

I am using the command like LongPhase/longPhase phase -s hg001_longshot.vcf.gz -b HG001_NBT2018_Guppy_4.2.2.bam -o lp_001 -r hg38.no_alt.fa -t 40 --ont the data used is just 8X ONT aligned to hg38, and the SNP calling result using longshot default parameters. HG001 ONT reads: https://s3-us-west-2.amazonaws.com/human-pangenomics/NHGRI_UCSC_panel/HG001/nanopore/Guppy_4.2.2/HG001_NBT2018_Guppy_4.2.2.fastq.gz hg38 reference: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/hg38.no_alt.fa.gz

twolinin commented 2 years ago

Hi, Can you help me decompress hg001_longshot.vcf.gz into hg001_longshot.vcf and run the program once?

yekaizhou commented 2 years ago

thanks a lot. it worked out.

ythuang0522 commented 2 years ago

Though it worked, we should note that 8x is really low coverage. >30x is usually recommended.