User: e.benn

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e.benn60
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Posts by e.benn

<prev • 11 results • page 1 of 2 • next >
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Comment: C: GNU parallel error: Command line too long
... presumably sooner or later the cat line itself will be too long. A lot of commands accept an argument, or a file that contains arguments eg grep -f {file}, curl -F abc=@file. Sadly cat doesn't seem to be one of them. You could stack another parallel: ```echo "parallel -k -a file_of_paths cat | m ...
written 1 day ago by e.benn60
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Comment: C: How to make this specific "pileup" like plot?
... Why not contact the author directly? https://profiles.ucsd.edu/sebastian.preissl ...
written 7 weeks ago by e.benn60
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Are secondary alignments used by any tool?
... I am trying to work out what tools use the secondary alignment feature of the sam format. My understanding is that there will always be exactly 1 primary alignment for each read, and secondary alignments could arise because the aligner cannot decide the exact best alignment. Does BWA / other aligne ...
alignment written 7 weeks ago by e.benn60 • updated 7 weeks ago by h.mon20k
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Answer: A: ROC curves from hap.py
... I had to trawl through the source, but I found out that rtg vcfeval is the tool that does the actual roc data generation. That tool requires INFO.VQSLOD (or FORMAT.XXX). https://github.com/Illumina/hap.py/pull/58 ...
written 3 months ago by e.benn60
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Comment: C: All of the lines in my file are part of the header / no alignment section
... What is the code above trying to do? Filter for certain regions? See `gatk PrintReads -L` or `samtools view -L` on how to do this using various region specifying files (beds vcfs etc). Also did the output of BWA contain data apart from the header? You only mention the output of your java code. Ano ...
written 3 months ago by e.benn60
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Comment: C: All of the lines in my file are part of the header / no alignment section
... "Fourth, I applied the java code to find the start and end coordinates of the exons and apply them" You attempted to filter the output of BWA to exon-only regions? And the output of this command was no data. It seems like your filter was wrong in some manner. If you don't post the actual commands yo ...
written 3 months ago by e.benn60
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Comment: C: All of the lines in my file are part of the header / no alignment section
... Please post the command line args, especially `samtools view -H` would cause this. ...
written 3 months ago by e.benn60
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ROC curves from hap.py
... https://github.com/Illumina/hap.py/blob/master/doc/happy.md#roc-curves I am trying to generate a roc curve with hap.py. The docs are a little confusing, I am wondering if anyone can help me decipher. I have asked on the github also: https://github.com/Illumina/hap.py/issues/57 There are two parame ...
illumina roc hap.py written 3 months ago by e.benn60
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Comment: C: Does BWA mem ever edit data
... Yes very good, I also need to keep the alignment, and the 'which pair-end' metadata, and probably some more I have forgotten. ...
written 4 months ago by e.benn60
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Comment: C: Does BWA mem ever edit data
... Thanks Andrew for that detailed answer, I will have a close look at all this ...
written 4 months ago by e.benn60

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Scholar 3 months ago, created an answer that has been accepted. For A: ROC curves from hap.py

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