Spiking variants into BAM file

Hi,

is anyone aware of any other tools than the following for spiking variants into BAM Files? I have tried them and there are some issues with each... I think I can manage but maybe there is another one that I missed?

Thanks, Manuel

bam

• 976 views • link

updated 4.1 years ago by benformatics

• written 4.1 years ago by Manuel

what are the issues?

• 0 views • link

written 4.1 years ago by benformatics

0 answers

No answers yet.

More posts like this

Visualize and explore eventalign data against reference
written 2.7 years ago by noodle

Hi all, Is anyone aware of a tool (GUI or python/R/bash package) to explore eventalign nanopore data (or fast5 raw data) with the corresponding alignment …
Somatic truth set
written 3.4 years ago by samuel

Does anyone know if there is a somatic truth set vcf available? I know there are now several available for germline samples from [GIAB][1] I …
Very high variant similarity between a couple
written 4.5 years ago by asalimih •

Hi, I've encountered a couple's whole exome sequencing data (Consanguineous marriage - Cousins ) which there seems to be a very high similarity between their …
How to modify a BAM file to avoid double-counting of variants from overlapping PE reads?
written 5.5 years ago by lechu •

Hi, I need to find a way to avoid counting the same mismatch twice in cases when it (the mismatch) lies on the overlapping part …
GLIBC error when trying to use sra-toolkit
written 6.2 years ago by amitfinkelstein •

I'm trying to download the latest sra-toolkit from NCBI on a remote server running **"Debian GNU/Linux 7 (wheezy)"**. I tried following the instructions in https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit, …
QUAST ignoring bam files
written 6.7 years ago by liorglic

Hello, I am having some trouble when I try to give QUAST pre-computed alignments with the --bam option. I have opened [an issue][1] on the …
converting FPC maps to CMAP format
written 8.3 years ago by bradford.condon •

I have an [FPC formatted][1] map file. I am installing [CMAP-js][2] on a website to display said map. Is anyone aware of an existing utility …
BAMSurgeon error report: bam readcount < fastq readcount, alignment sanity check failed!
written 9.1 years ago by jing.mengrabbit •

Hi, I ran BAMSurgeon (https://github.com/adamewing/bamsurgeon), and it gives the following error report: ERROR 2017-07-06 09:03:39.934250 encountered error in mutation spikein: ['chr1_27691816_27691816_0.5_None'] Traceback (most recent call …
Converting large (compressed and unsorted) BAM files to fastq
written 9.7 years ago by alesssia

Dear all, we got a few hundred large compressed BAM files (70GB <= size <= 300GB). They are not sorted and we would like to …
Anyone used BAMSurgeon to spike in 1KB insertions/deletions?
written 10.9 years ago by sichan

Hi Everyone, I'm interested in using [BAMSurgeon][1] to spike in structural variants up to 1KB in length to my BAM. Here's my command: python addsv.py …