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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Difficulties detecting 1 nt deletions in PacBio data #1922

Open JarrigeD opened 1 year ago

JarrigeD commented 1 year ago

Hello,

I am trying to use bcftools 1.17 to call variants in bacterial genomes with PacBio CCS data.

I attempted to use the mapped CSS reads, but kept running into segmentation fault errors and got troncated results. So I opted to assemble the reads first and to use mpileup and call afterwards.

It seems to work for substitutions and larger indels. However, I tried many parameters and cannot find a way to detect 1 nucleotide deletions. Here is one of them in IGV:

E1_3400667_undetected_indel

And here is the command I used:

srun -p fast -c 8 bcftools mpileup --threads 8 --skip-any-set UNMAP --ambig-reads incAD0 --indel-bias 2.0 -m 1 --fasta-ref genome.fasta mapping/xxx_sorted.bam | bcftools call --ploidy 1 -m -v > variants/xxx_bcftools.vcf

Is there a way to detect those small indels in long read assembly data with bcftools?

Thank you and have a nice day.

pd3 commented 1 year ago

We'd need a small test case to debug this, unfortunately can't help just from the screenshot.