Questions tagged [mpileup]
The mpileup tag has no usage guidance.
13
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Make mpileup file with several BAM files
I'm new to this business, so my question may seem as dumb. I want to make an mpileup file using a reference sequence and several (two to begin with) aligned sorted BAM files. And I want the output ...
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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 ...
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How do I call variants using BCFTools without piping mpileup file?
I need to call variants on a large number of reads using both VarScan2 and BCFTools. Both of these variant calling tools use <...
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How to generate a consensus sequence from a multi-reference BAM file?
I am trying to generate a consensus sequence from a BAM file that was generated by mapping reads to a reference FASTA containing multiple sequences.
Usually, I generate consensus sequences from BAM ...
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Is there a tool that can perform a read-group-aware mpileup from a single file?
I would like to perform a samtools mpileup from a single file that contains thousands of read groups with different SM tags. I could split the bam by read group ...
- 2,216
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Generate VCF from different .bam files with different chromosome names
I have two resources of .bam files. One is generated by our lab (1 sample = 1 bam). One is downloaded online (again 1 sample = 1 bam). For the downloaded samples the chromosomes are labelled: chr1, ...
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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 (...
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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 ...
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What is a samtools mpileup reference skip?
The samtools documentation for mpileup states:
At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a '>' or '<' for a ...
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samtools mpileup skipping read
I run the command:
samtools mpileup -O -s -q20-B -Q20 -f hg19.fa -r chr1:569929-569931 myFile.bam
and get:
...
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I am getting this error when running a test data set for Lyve-SET on RHEL 7. Is this an MPileup error or something else?
This is the error that I am getting:
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variant calling on ChIP-seq style data: samtools mpileup with minimal filters
I am running samtools mpileup (v1.4) on a bam file with very choppy coverage (ChIP-seq style data). I want to get a first-pass list of positions with SNVs and their frequency as reported by the read ...
- 2,294
7
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samtools mpileup empty when filtering out flags
I produced a bam file by aligning reads to a small set of synthetic sequences using bwa-mem.
I am heavily filtering reads that are not paired and of a certain orientation.
Applying the filtering, I ...
- 2,294