VariantBam
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walaj
Filtering and profiling of next-generational sequencing data using region-specific rules
Dear VariantBam developers, I ran the command `variant $bam -m 100 -o mini.bam -b` to obtain a maximum coverage of 50 along my sample, however when I visually inspected the...
 i want to exclude N >1000 reads for RNA bam files, for example, the reads "9ae8a1cd-1a71-40d1-ab06-f1567ec79f9a" contained 1593N, it should be filtered. However , this software not work when...
Hello, I am trying to run the program and am coming across this error. Do you have any advice? $ variant Sorted20130SAMy43Aligned.bam --motif Telomotifs.txt -b -o TelofromSorted.bam ...making the AhoCorasick...
The google cloud test file seems to have been moved somewhere else: `gsutil ls -l gs://isb-cgc-open/ccle/LUSC/DNA-Seq/C836.NCI-H1339.2.bam` `CommandException: One or more URLs matched no objects.` And the test/small.bam file is missing...
Hi, first -- **thank you** for your software! I am working with paired end sequencing on a pool of fragments that contain a large proportion of fragments shorter than the...
Jeremiah; Now that we have VariantBam maximum coverage downsampling in bcbio (thank you again), we've been working on doing benchmarking runs with and without downsampling. Because we need to run...
Hello, I try to build a `linux-aarch64` binary for Bioconda - https://github.com/bioconda/bioconda-recipes/pull/48763. I use https://github.com/DLTcollab/sse2neon/ to translate Intel SSE to ARM NEON. The build passes fine! ``` mgrigorov in 🌐...
Hi, Trying to use this tool on a sorted BAM file to subsample to a much lower coverage for testing. I'm getting the following error from the below command: variant...
