User: jane19

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jane190
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Posts by jane19

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Comment: C: contig order b37
... Hi, The first genome we tried was from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz I haven't opened it to check the ordering, so I'm not sure where it got messed up. BW, Jane ...
written 2.7 years ago by jane190
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Answer: A: contig order b37
... FYI. The rsync version of b37 was the same as mine (from 1000g) , but using importing as 'gatk' rather than 'as is' seemed to fix the problem. Thanks, Jane ...
written 2.7 years ago by jane190
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contig order b37
... Hi, I'm trying to use gatk on our own instance but get the error below. I have installed the b37 (hg_g1k_v37) genome and indexed and ran alignment with bwa-mem. When I try and run gatk unified genotyper I hit a problem. It looks like the MT chromosome is in the wrong order in the reference. I don ...
gatk alignment bwa written 2.7 years ago by jane190 • updated 2.7 years ago by Jennifer Hillman Jackson25k

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