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Fixing phasing snps arguments and LiftOver #149

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Fixing phasing snps arguments and LiftOver #149

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d9aeed1
Fix snp list argument when phasing
oriolpich Jul 20, 2022
50722c2
Fix liftover arguments from picard
oriolpich Jul 20, 2022
c6fe938
Remove dashes for latest picard compatibility
oriolpich Jul 20, 2022
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4 changes: 2 additions & 2 deletions src/hatchet/utils/phase_snps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,8 +247,8 @@ def liftover(self, infile, chromosome, outname, chain, refgen, ch):
# e.g. small contigs variably present among the assemblies

cmd1 = (
f'{self.picard} LiftoverVcf -I {infile} -O {tmpfile} -CHAIN {chain} -R {refgen} -REJECT {rejfile} '
'--WARN_ON_MISSING_CONTIG true'
f'{self.picard} LiftoverVcf I={infile} O={tmpfile} CHAIN={chain} R={refgen} REJECT={rejfile} '
'WARN_ON_MISSING_CONTIG=true'
)
# need to change 'chr' notation depending on liftover direction
c = chromosome if not ch else f'chr{chromosome}'
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2 changes: 1 addition & 1 deletion src/hatchet/utils/run.py
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Expand Up @@ -158,8 +158,8 @@ def main(args=None):
f'{output}/phase/',
'-L',
]
+ (['-N'] if config.genotype_snps.chr_notation else [])
+ glob.glob(f'{output}/snps/*.vcf.gz')
+ (['-N'] if config.genotype_snps.chr_notation else [])
+ extra_args
)

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