User: e.benn

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e.benn40
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e*****@garvan.org.au

Posts by e.benn

<prev • 8 results • page 1 of 1 • next >
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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 5 weeks ago by e.benn40
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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 5 weeks ago by e.benn40
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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 5 weeks ago by e.benn40
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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 5 weeks ago by e.benn40
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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 5 weeks ago by e.benn40
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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 8 weeks ago by e.benn40
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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 9 weeks ago by e.benn40
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Does BWA mem ever discard or modify data
... I could not find a definite answer to this question. Does BWA mem modify the data it receives? I understand that it adds data (alignment of course, and more), but am wondering if the data in the fastq is guaranteed to survive. The program takes in read names, a sequence string, and a quality string ...
bwa written 9 weeks ago by e.benn40

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Scholar 5 weeks ago, created an answer that has been accepted. For A: ROC curves from hap.py

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