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Questions tagged [samtools]
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
We're preparing to analyze thousands of
.bam files beginning with re-alignment, sorting, etc.
Complicated question: Has anyone investigated the optimal thread and ...
Feb 10, 2022 at 4:36
I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R.
Samtools/BCFtools (Heng Li) provides a Perl script ...
Nov 12, 2017 at 10:27
EDIT: I do not want to make any modifications to the mapped reads, I simply want to ignore one read in a read pair if they overlap the same region.
I used samtools depth to calculate the depth of ...
Nov 12, 2018 at 23:26
I have a text file 'qnames.txt' with QNAMEs in the following format:
I would like to ...
Jan 23, 2018 at 18:41
I have few BAM files which are generated from Ion Torrent Server (ampliseq) aligned to hg19 genome. I want to extract read counts from the bam files and I know that "featureCounts" can be used for ...
Dec 14, 2017 at 9:41
I am currently working on my own Metagenomic pipeline, utilizing Bowtie 2 to map. Bowtie 2 outputs a SAM file, which I convert to a .BAM and sort it using Samtools. When I try to utilize Samtools to ...
Sep 21, 2018 at 0:39
Related to my other question (Samtools sort: most efficient memory and thread settings for many samples on a cluster), we need to optimize
samtools sort as we ...
Feb 10, 2022 at 5:02
I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
Jul 25, 2020 at 0:53
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