bamUtil
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statgen
Dear bamUtils, I'm using `bam clipOverlap --stats --poolSize 100000000 --in PE.bam --out merge.bam` and get reports like the below for a handful of files. The alignments all look clean before...
Hi, I am wondering if I am using the tool correctly. Will there be a record for every `QNAME` in the bams being compared when comparing `MAPQ` scores? I am...
Hi, I installed this tool but it's empty with conda, can you give me some suggestions?
Hello,I meet a problem:bash -x testBam2FastQ.sh and bash -x testMergeBam.sh failed on centos8_aarch64 ```console aarch64: [root@localhost test]# bash -x testMergeBam.sh + ERROR=false + ../bin/bam mergeBam --out results/mergeBam.bam --list testFiles/mergeBam.list --noph...
Hi, i recently use bamUtil to extract reads to be paried-read fastq files from bam file. They found read pairs but the generated fastq files are empty. `bam bam2FastQ --in...
I'm working on a Linux based HPC working with private data hence the environment is restrictive (no internet connection); therefore packages must be built from source. After downloading the file...
Hi, I have two BAM files that I'd like to compare. Each is about 5.6GB. I expect them to be identical (I'm sort of doing a reproducibility test). When I...
It would be great if `bam diff` returns an exit code (0 for identical, 1 for different) just like the `diff` command does. This will allow us to do something...
If the compiler toolchain is in a non-standard location, the current Makefile does pick up the correct system includes from CFLAGS, but does not use the corresponding `-L` from LDFLAGS....
``` samtools view ... | bam trimBam -.ubam -.ubam --clip -R ``` produces this error: ``` bam: invalid option -- '.' ERROR: Unrecognized option left ``` works ok with ```...
