Convert mutation file to VCF

Question

[Ron]

Hi all,

I am working on mutation analysis on RNAseq data.I used rnaseqmut for this purpose: https://github.com/davidliwei/rnaseqmut

From the link above

III. Demo: detecting mutations from a series of RNA-Seq BAM files

I am stuck at 5th step since I don't have normals and only have tumors,I am not getting a VCF output from this step. I tried adding some dummy normals in the ALLMUT.txt file(generated after 4th step) and am able to get a VCF - confirming the command is fine when you have normals .

Commands when with Normals:

CONTROLGROUP="18,19"
LABELS="TUMOR1,TUMOR2,TUMOR3,TUMOR4,TUMOR5,TUMOR6,TUMOR7,TUMOR8,TUMOR9,TUMOR10,TUMOR11,TUMOR12,TUMOR13,TUMOR14,TUMOR15,TUMOR16,TUMOR17,NORMAL1,NORMAL2,TUMOR18,TUMOR19,TUMOR20,TUMOR21,TUMOR22,TUMOR23,TUMOR24,TUMOR25,TUMOR26,TUMOR27,TUMOR28,TUMOR29,TUMOR30,TUMOR31,TUMOR32,TUMOR33,TUMOR34,TUMOR35,TUMOR36,TUMOR37,TUMOR38,TUMOR39,TUMOR40,TUMOR41,TUMOR42"



python software/rnaseqmut-master/script/filtermut.py -t 1 -f 0.2 -d 10  -b 0 -c $CONTROLGROUP  -l $LABELS < $destdir/ALLMUT.txt > $destdir/ALLMUT_FILTERED.vcf


**Commands when with out Normals**



LABELS="TUMOR1,TUMOR2,TUMOR3,TUMOR4,TUMOR5,TUMOR6,TUMOR7,TUMOR8,TUMOR9,TUMOR10,TUMOR11,TUMOR12,TUMOR13,TUMOR14,TUMOR15,TUMOR16,TUMOR17,TUMOR18,TUMOR19,TUMOR20,TUMOR21,TUMOR22,TUMOR23,TUMOR24,TUMOR25,TUMOR26,TUMOR27,TUMOR28,TUMOR29,TUMOR30,TUMOR31,TUMOR32,TUMOR33,TUMOR34,TUMOR35,TUMOR36,TUMOR37,TUMOR38,TUMOR39,TUMOR40,TUMOR41,TUMOR42,TUMOR43,TUMOR44"


python software/rnaseqmut-master/script/filtermut.py -t 1  -d 10    -l $LABELS < $destdir/ALLMUT.txt > $destdir/ALLMUT_FILTERED.vcf

Let me know if anyone has experience using this software without Normals. Basically,if I am able to convert this file from Step4 to VCF,that should solve the final purpose of annotating VCF file.

Thanks,

Ron