StackOverflow Questions for Tag: samtools

Rafail Adam

Reputation: 1

How do I resolve the "inconsistent chromosome block error?

bioinformaticssamtools

Score: 0

Answers: 0

Theresa

Reputation: 75

Snakemake: MissingInputException in rule - Missing input files for rule sam_to_bam:

inputworkflowsamplesnakemakesamtools

Score: 0

Answers: 1

Somu

Reputation: 25

Split a SAM file in Awk keeping N number of lines as header

awkbioinformaticssamtoolsbam

Score: 2

Answers: 1

Jeanie

Reputation: 21

How to find the base using the chromosome number and position?

pythonbioinformaticsdna-sequencevcf-variant-call-formatsamtools

Score: 0

Answers: 1

Caroline

Reputation: 167

Extracting information from a file using another file with list of specific text; Ubuntu/ Linux

bashbioinformaticsfastasamtools

Score: 2

Answers: 2

Ralph matar

Reputation: 35

MissingOutputException snakemake

snakemakesamtoolsbam

Score: 1

Answers: 1

PaulaO

Reputation: 67

Is there any way to pass a bed file or similar with target regions to samtools coverage?

samtools

Score: 1

Answers: 1

Roy Khair

Reputation: 1

bash commands don't run from R Markdown file

rbashr-markdownsamtools

Score: 0

Answers: 0

P. Solar

Reputation: 359

Wrong plotting data (insert size vs base quality means from BAM file)

pythonmatplotlibplotsamtoolspysam

Score: 0

Answers: 0

Pei-Wei Sun

Reputation: 47

How to locate the position of non-missing sequence in the fasta

fastasamtools

Score: 1

Answers: 1

PaulaO

Reputation: 67

Find sequencing reads with insertions longer than number

sequencingsamtoolsbam

Score: 1

Answers: 1

Rotomegax

Reputation: 27

My merge overlapping coordinate python script cost too much memory

pythonsamtools

Score: -1

Answers: 1

Mauro

Reputation: 107

bcftools mpileup failed, format error of index

samtoolsbcftools

Score: 3

Answers: 1

Megan

Reputation: 15

Using SAMtools and storing outputs for a large number of files

bashloopsshellunixsamtools

Score: 1

Answers: 1

Timur Shtatland

Reputation: 12337

How to activate conda environment in GitHub Actions?

installationcondagithub-actionsenvironmentsamtools

Score: 11

Answers: 2

Atsathe

Reputation: 1

Samtools not working after system update (libcrypto.1.0.0.dylib' (no such file))

condapython-3.9anaconda3samtools

Score: 0

Answers: 1

Hrishikesh Hardikar

Reputation: 119

How to retain reads on only an certain size in a bam file?

bioinformaticssamtoolsbam

Score: 2

Answers: 1

Aragaki

Reputation: 41

Problem of running samtools in python using subprocess.run()

pythonsubprocessbioinformaticssigabrtsamtools

Score: 0

Answers: 2

willbrew

Reputation: 1

I have 2 bash loops with the same structure and only the first works

bashfor-loopsamtools

Score: 0

Answers: 0

twinsinc

Reputation: 173

How to use pysam.view() to convert SAM to BAM

pythonsamsamtoolspysambam

Score: 1

Answers: 2

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StackOverflow Questions for Tag: samtools

How do I resolve the &quot;inconsistent chromosome block error?

Snakemake: MissingInputException in rule - Missing input files for rule sam_to_bam:

Split a SAM file in Awk keeping N number of lines as header

How to find the base using the chromosome number and position?

Extracting information from a file using another file with list of specific text; Ubuntu/ Linux

MissingOutputException snakemake

Is there any way to pass a bed file or similar with target regions to samtools coverage?

bash commands don&#39;t run from R Markdown file

Wrong plotting data (insert size vs base quality means from BAM file)

How to locate the position of non-missing sequence in the fasta

Find sequencing reads with insertions longer than number

My merge overlapping coordinate python script cost too much memory

bcftools mpileup failed, format error of index

Using SAMtools and storing outputs for a large number of files

How to activate conda environment in GitHub Actions?

Samtools not working after system update (libcrypto.1.0.0.dylib&#39; (no such file))

How to retain reads on only an certain size in a bam file?

Problem of running samtools in python using subprocess.run()

I have 2 bash loops with the same structure and only the first works

How to use pysam.view() to convert SAM to BAM

How do I resolve the "inconsistent chromosome block error?

bash commands don't run from R Markdown file

Samtools not working after system update (libcrypto.1.0.0.dylib' (no such file))