7
votes
Accepted
variant calling on ChIP-seq style data: samtools mpileup with minimal filters
I used this in the past for ChIP-seq data and it generated SNVs:
...
- 2,169
5
votes
variant calling on ChIP-seq style data: samtools mpileup with minimal filters
Another approach is htsbox. You can get a candidate list with:
htsbox pileup -Cvcf ref.fa -q20 -Q20 -s5 file.bam > out.vcf
Here, ...
- 6,485
5
votes
Accepted
What is a samtools mpileup reference skip?
That documentation has been expanded recently (see PR #1055) and now describes the characters seen in this column in more detail:
...
- 956
3
votes
Accepted
Make mpileup file with several BAM files
Have you tried using samtools mpileup in.bam [in2.bam [...]]? Here's information about the output format from the manual page:
The first three columns give the ...
- 13.8k
3
votes
Accepted
samtools mpileup skipping read
Examining the mpileup output for a single read on its own is a good way to figure out why bases are not appearing as expected.
So if you suspect that the ...
- 956
3
votes
samtools mpileup skipping read
Why do you believe it's the read with cigar=18S58M? The mapping qualities given in sam files are different to those in the mpileup output. I guess samtools is doing ...
- 1,342
2
votes
Accepted
samtools mpileup empty when filtering out flags
By using -h in the samtools view command, you're including all the header lines in your word count. If you happen to have about ...
- 13.8k
2
votes
How do I call variants using BCFTools without piping mpileup file?
Why not use tee? Please see this post.
You can write mpileup to file while also piping it to another process. For example, ...
- 1,105
2
votes
Accepted
Is there a tool that can perform a read-group-aware mpileup from a single file?
I broke down and finally scratched this itch. I have implemented a tool that performs read-group-aware text-pileup from a single SAM/BAM file. The tool is called streaming_pileupy and it's available ...
- 2,236
2
votes
Generate VCF from different .bam files with different chromosome names
The main issue here is that your bam files have different chromosome labels. (i.e. 1,2,3 vs. chr1,chr2,chr3) as you mentioned.
This suggests that the data was mapped to a slightly different version ...
- 71
1
vote
How do I call variants using BCFTools without piping mpileup file?
Bcftools and samtools both follow the very common Unix filter pattern: they read from all input files specified (as non-option plain arguments), or if there are none they read from standard input.
<...
- 956
1
vote
What is a samtools mpileup reference skip?
Skipped references are similar to deletions, but the different symbols used are indicating that it's an expected deletion. The most common use for a skipped reference is when excluding intronic ...
- 13.8k
1
vote
Generate VCF from different .bam files with different chromosome names
I am not familiar with getting variants from bam files, so I will just answer the second part. From the error message, it seems that it is necessary to have consistent chromosome labels across ...
- 857
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