Question: Samtools Filter Pileup "Only Report Variants?" Option Is Misleading
gravatar for Jesse Erdmann
6.8 years ago by
Jesse Erdmann60 wrote:
In using the filter pileup tool we've discovered that the option "Only report variants?" will throw away lines that have indels provided that they do not contain any SNPs. For example the line: chr1 88427041 C 38 ..+1A..+1A.....+1A.,..+1A.....,.+1A,.,......,...,^~.^~,^~,^~, HHHHHFEHHHHHBFHHHHHHBFHHHEHHHAHHHFHG#E will not be included in the filtered results. At the very least we would recommend relabeling the option to "Only report SNP variants?" But it would also be helpful to include an option to filter for both SNP and indel variants. Thanks! -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota 612-626-3123
snp • 1.1k views
ADD COMMENTlink modified 6.8 years ago by Jennifer Hillman Jackson25k • written 6.8 years ago by Jesse Erdmann60
gravatar for Jennifer Hillman Jackson
6.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Jesse, We agree that the original "pileup" tool does not have all of the functionality that one might want. The tool authors seem to also agree, and developed an upgraded version called "mpileup". This has recently been wrapped and added to the Galaxy main public instance in the same 'NGS: SAM Tools' tool group. The 'MPileup SNP and indel caller' tool form has a summary of the available options and links to the full documentation, including the SAMTools' authors and support/discussion groups. Thanks for the feedback and hopefully you will find the Mpileup tool useful and/or SAMTools discussion groups a helpful resource, Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.8 years ago by Jennifer Hillman Jackson25k
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