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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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convert supplementary reads to primary in sam or bam

I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
Fini's user avatar
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4 votes
0 answers
136 views

Write a bash script to run gatk, fix errors with input, and rerun until completion

I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating: ...
kylep's user avatar
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3 votes
0 answers
571 views

How to analyze an IGV alignment

I'm working on a project where I am analyzing the performance of an alignment workflow. My goal is to find regions in the resulting BAM file where there are outstanding discrepancies or anything that ...
pythonbeginner44's user avatar
2 votes
0 answers
139 views

Difference between pileup and mpileup in VarScan and samtools

I'm going to call variants with VarScan from a pileup files created with samtools. I realized that there are in general two major possibilities to call variants, pileup as well as mpileup. The VarScan ...
Anti's user avatar
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2 votes
0 answers
382 views

How to extract reads that map exclusively to a single site with 1 or zero mismatches from BAM files

I generated BAM files (sorted by coordinates) by aligning human RNA reads against the human reference genome using BWA MEM and ...
plicht's user avatar
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2 votes
0 answers
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Which R package to use for differential analysis with TPM values?

I'm using hisat2, stringtie tools for the RNA-Seq analysis. After stringtie using ballgown I get FPKM and TPM values for every gene. I have seen that edgeR, Deseq2 can be used for Counts data. I ...
beginner's user avatar
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2 votes
1 answer
86 views

Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?

This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback on question format appreciated. I have ...
Liam McIntyre's user avatar
1 vote
0 answers
196 views

Mapping statistics from the bam files

I would like to find the mapping statistics from the sorted bam files. Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
Kam's user avatar
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1 vote
0 answers
44 views

How do I filter reads from a bamfile based on 5' and 3' ends?

I have data in paired-end as well as single-end format for the same sample.I would like to split those two files into two per each, where one contains sequences that have 5' end and the other one has ...
Pikabu's user avatar
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1 vote
0 answers
134 views

Trinity de novo transcriptome assembly: samtools view failed to add PG line to the header

I have assembled the transcriptome a plant species using Trinity. Here is the command: ...
Faroll's user avatar
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1 vote
0 answers
866 views

Conversion of SAM to BAM files

I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file . The command I am using to make very ...
Aranyak Goswami's user avatar
1 vote
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48 views

Indel quality from mpileup

Could someone please confirm that I understand this correctly? I have the res and qual columns from mpileup and I would like to match them to get the qual per base. It seems that the indel initiation (...
Liam McIntyre's user avatar
1 vote
0 answers
337 views

bedtools single-nucleotide coverage in BED-specified regions for multiple BAMs

I have a BED6 (BED + name, score, strand info) file that defines some regions of interest. I also have a set of BAMs corresponding to different samples. I would like to obtain output similar to <...
merv's user avatar
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0 votes
0 answers
141 views

seqff script got trouble after samtools treatment

I'm trying to study fetal fraction by using a seqff script from here. The instruction says that I need a headless sam file to work so after alignment with bwa, I process my sam file by using samtools: ...
khanhlpbao's user avatar
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151 views

summarising read group information from a .bam file

I have merged together 2 different .bam files in order to simulate sample contamination. So the reads can come from one of two samples, as shown by the read group info: ...
user438383's user avatar
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