Questions tagged [mpileup]

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Discrepancy in Depth of Coverage Estimation between Pileup and samtools depth

I'm encountering a discrepancy in the depth of coverage assessment for specific coordinates when comparing results obtained from pileup files and samtools depth. I've processed pileup files and ...
Irina's user avatar
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0 votes
1 answer
255 views

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 ...
Vasily's user avatar
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2 votes
0 answers
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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 ...
Anti's user avatar
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1 vote
2 answers
585 views

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 <...
PPrasai's user avatar
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2 votes
1 answer
2k views

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 ...
teaelleceecee's user avatar
4 votes
1 answer
281 views

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 ...
winni2k's user avatar
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1 vote
2 answers
775 views

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, ...
user3329732's user avatar
1 vote
0 answers
47 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
2 votes
1 answer
85 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
4 votes
2 answers
597 views

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 ...
mattm's user avatar
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5 votes
2 answers
424 views

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: ...
aerijman's user avatar
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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: ...
Drops's user avatar
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7 votes
2 answers
313 views

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 ...
719016's user avatar
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7 votes
1 answer
468 views

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 ...
719016's user avatar
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