davidliwei / rnaseqmut Goto Github PK

I test a bam file with indel reads, and all the reads has a MD tag. If the reference fasta file is provided, the reference base in the ouput will be the correct one. But if I do not provide the reference sequence, and let rnaseqmut infer that from the MD tag., then some position can no be inferred correctly.

Demo run without reference seq:

(The 4th row in the output show ref base of pos:4 is G, while it should be C)

$ rnaseqmut -s 6 -m 3 -i 1 -k test.bam | head -5

rRNA-RNA18SN1   3       C       G       35      0       4       0
rRNA-RNA18SN1   3       C       A       35      0       2       0
rRNA-RNA18SN1   4       C       T       45      0       1       0
rRNA-RNA18SN1   4       G       T       45      0       1       0
rRNA-RNA18SN1   5       T       G       38      0       4       0

Demo run withreference seq:

$ rnaseqmut -s 6 -m 3 -i 1 -k -r test.fa test.bam | head -5

rRNA-RNA18SN1   3       C       G       36      0       4       0
rRNA-RNA18SN1   3       C       A       36      0       2       0
rRNA-RNA18SN1   4       C       T       45      0       1       0
rRNA-RNA18SN1   5       T       G       42      0       4       0
rRNA-RNA18SN1   5       T       A       42      0       1       0

demo files: test.tar.gz

Hi!
Thanks a lot for you work on rnaseqmut, so useful!
I'm trying to find mutations from rnaseq data. When I obtain my mutation list from bam file, I find some mutation positions corrisponding to a cromosome but with the value "-1". I do not observe no "-1" in files generated from demo bam files. What does it means "-1"?
Thanks in advance,
Francesco

Hi there,
Thanks for the brilliant work on rnaseqmut! Been trying to call variants on a single BAM file and I get a tab delimited file in the output, so step 1 working fine. However, when I pass this text file to filtermut.py I get nothing in the output. Have you got any guidelines on how to simply produce vcf files from rnaseqmut? Are you planning on adding any of the fields usually coming from tools such as FreeBayes and Gatk, like AD and DP etc.?

Much appreciated,
Thanks,
Miika

I think it would be better if non-mutated sites can also show up in the result, when -i flag is set to 0?