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Hi Pamela Bretscher, yes I think so. Thanks.
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Solution: gatk --java-options "-Dsamjdk.compression_level=6" ApplyBQSR [options]
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I was able to get a ~25% filesize reduction with running the bam file through samtools view. However, trying to use "ApplyBQSR --java-options "-Dsamjdk.compression_level=6" results in error: Error:...
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This might work: samtools view -@ 6 -h -b --output-fmt-option level=6 -o compressed.bam uncompressed.bqsr.bam You should be able to leave out "--output-fmt-option level=6" and it should work just ...
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Compression level 2 effectively doubles the file size. I would be interested to know what kind of speed advantage are we talking about here to outweigh this massive waste of disk space. The BQSR pr...
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Thanks for the explanation. For cancer heterogeneity analysis, this is the exact opposite functionality that is required. I think SelectVariants should have some option to remove undetected variant...
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Nope... this still leaves in variants like: GT:AD:AF:DP:F1R2:F2R1:SB 0/1:52,0:0.019:52:26,0:26,0:35,17,0,0 I think there might be a bug somewhere in Mutect that sets the GT field erroneously to "0/1".
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Having "##fileformat=VCFv4.2" at the beginning of the --alleles .vcf.gz file seems to have done the trick.
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The "-sn" flag is just the short version of "--sample-name".
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My next idea was to do further filtering based on the AF in the sample data which is "9.123e-03" in the above example row (chr2 70143941)... Looks like SelectVariants adds "AC=1;AF=0.500;AN=2" to ...