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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,

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2 votes
2 answers

Samtools sort: most efficient memory and thread settings for many samples on a cluster

We're preparing to analyze thousands of .bam files beginning with re-alignment, sorting, etc. Complicated question: Has anyone investigated the optimal thread and ...
Mark Ebbert's user avatar
  • 1,274
11 votes
3 answers

Converting a VCF into a FASTA given a reference with Python, R

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 ...
ShanZhengYang's user avatar
9 votes
4 answers

Double-counting coverage of overlapped read pairs

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 ...
d_kennetz's user avatar
  • 631
8 votes
7 answers

How to subset a BAM by a list of QNAMEs?

I have a text file 'qnames.txt' with QNAMEs in the following format: EXAMPLE:QNAME1 EXAMPLE:QNAME2 EXAMPLE:QNAME3 EXAMPLE:QNAME4 EXAMPLE:QNAME5 I would like to ...
EB2127's user avatar
  • 1,373
6 votes
1 answer

Read counts from BAM file

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 ...
stack_learner's user avatar
4 votes
1 answer

Error given while trying to index a BAM file with Samtools Index - NO COOR?

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 ...
user avatar
2 votes
1 answer

Samtools sort: most efficient approach to sort a single sample after aligning split .fastq files

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 ...
Mark Ebbert's user avatar
  • 1,274
1 vote
1 answer

Samtools Index: Chromosome Blocks not Continuous

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 ...
annabelperry's user avatar