User: richyanicky

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richyanicky10
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Posts by richyanicky

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Failed to liftover from hg38 to hg19
... Hello. I am attempting to convert from hg38 to hg19. My results so far are picard rejects all. CrossMap.py does convert some but fails because of this in the chain file. > > File "/usr/local/bin/CrossMap.py", line 1932, in > crossmap_vcf_file(mapping = mapTree, infile= in_file, ou ...
written 11 months ago by richyanicky10
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Comment: C: plink2 bgen to vcf ukbiobank
... Yes I used the comment below by chrchang253 and it worked.. ...
written 11 months ago by richyanicky10
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using samtools to verify tabix. Query in python generates error.
... I have the following file with index : -rw-rw-r-- 1 ryanicky ryanicky 335M Nov 22 16:15 multiallel.csv.gz drwxrwxrw- 18 ryanicky root 4.0K Nov 22 16:17 . -rw-rw-r-- 1 ryanicky ryanicky 70 Nov 22 16:32 multiallel.csv.gz.tbi When I run the following in p ...
python tabix samtools written 15 months ago by richyanicky10 • updated 15 months ago by ATpoint46k
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Comment: C: Strands are reversed
... That cleared up the issue Thank You! ...
written 20 months ago by richyanicky10
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Strands are reversed
... Hello, I have converted a Ukbiobank bgen file to vcf for processing against a reference panel using beagle. to make the pgen file from bgen I used the following. plink2 --bgen ukb_imp_chr17_v3.bgen --sample ukb####_imp_chr17_v3_s#####.sample --make-pgen --keep-allele-order There is a message ...
plink beagle written 20 months ago by richyanicky10 • updated 20 months ago by GenoMax96k
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Answer: A: vcf file format
... In plink2 there is a vcf-4.2 option . * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are present, they are automatically merged with chrX, with proper handling of chromosome codes and male ploidy. When the 'bg ...
written 21 months ago by richyanicky10
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plink2 bgen to vcf ukbiobank
... Hello I have imputed data from ukbiobank in bgen format. I would like to convert it to a vcf file. I can use plink2 to make pgen files and then use plink2 again to create a vcf plink2 --bgen ukb_imp_chr17_v3.bgen --sample ukimp_chr17_v3_s.sample --make-pgen plink2 --pgen plink2.pgen --pv ...
software error written 21 months ago by richyanicky10 • updated 10 months ago by bcole40

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