I'm using pindel on a set of sample pairs aligned using bwa mem but it doesn't make a good usage of the specified threads. In addition it seems to take too long to process a single chromosome. When I run pindel on the same samples but aligned using bwa aln the profile of multithreaded usage is completely different and much more efficient.
Is it possible that pindel doesn't make a good usage of the new flags in the bam reported by bwa mem, since now it's possible to find multiple primary alignments for a split read and the new supplemental flag 0x800?
A typical call to pindel is:
pindel-0.2.5a3 -f /path/to/hg19.fa -i /path/to/config.txt -o my_sample -c Y -T 8
Also mention that the argument -M was not set in the alignment of the samples with bwa mem.
Best,
Xavier
•
written
by
Xavier Pastor •
0 answers
No answers yet.
Log in to answer this question.
-
BWA MEM different synthax on linux (bash) and macOS (zsh)
written by gernophil •
-
BWA mem minimum read length
written by yolek64754 •
-
Pindel segmentation error
written by amyruthvandiver •
-
can I map multiple (>2) fastq reads against and assembly using bwa?
written by sa91 •
-
Fastq screen: use bwa aln and not bwa mem
written by Matteo •
-
BWA-mem alignment is not giving desired output
written by micro32uvas •
-
BWA mem and BWA aln lead to different results
written by zhangdezhi008 •
-
bwa mem on a bam file
written by vimartin •
-
When and why is bwa aln better then bwa mem?
written by dariober
-
Pindel Bad_Alloc Error With Window Size 1
written by Jack •
I'd just like to mention that after removing the supplemental reads in the bwa mem alignment (samtools view -bh -F 0x800) pindel seems to behave similar as to bwa aln alignments, at least computationally. I still need to confirm how about the final results.
If this is true I guess my initial suspicion was true and pindel cannot deal well with bam files reporting several primary alignments for the same read.
Best,
Xavier