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tgen / CovGen

Creates a target specific exome_full192.coverage.txt file required by MutSig
MIT License
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CovGen generates a coverage file with ALL 0 values for the coverage #10

Open ruhollah2 opened 3 years ago

ruhollah2 commented 3 years ago

Hi there,

I am trying to use CovGen on my mouse tumor WES samples to generate the coverage file for MutSig analysis.

The CovGen-generated coverage file _exome_full192.coverage.txt shows 0 for all rows under the coverage column. What is wrong?

Using or not using -b switch (to filter out or not poorly captured exome in target space based on 6 BAM files) does not make any difference

here is my command:

./CovGen -o ruh_covgen_prefix \
-f  Mus_musculus.GRCm38.dna.primary_assembly.fa \
-g ensembl_release92_GRCm38/Mus_musculus.GRCm38.92.chr.gtf \
-t Bait_Interval.bed  \
-s invivo/snpEff/  \
-v GRCm38.99

The -t is the bait bed file provided to us by the WES sequencing company (where we sent our tumor samples for sequencing, so that they sent us back the FASTQ & BAM files) Here is Ensembl GTF and FASTA files I used

Also all system requirement/dependencies mentioned in CovGen github are satisfied.

Here is the head of my output full coverage file generated by CovGen:

gene    effect  categ   coverage
ENSMUSG00000000001  noncoding   A(A->C)A    0
ENSMUSG00000000001  noncoding   A(A->C)C    0
ENSMUSG00000000001  noncoding   A(A->C)G    0
ENSMUSG00000000001  noncoding   A(A->C)T    0
ENSMUSG00000000001  noncoding   A(A->G)A    0
ENSMUSG00000000001  noncoding   A(A->G)C    0
ENSMUSG00000000001  noncoding   A(A->G)G    0
ENSMUSG00000000001  noncoding   A(A->G)T    0
ENSMUSG00000000001  noncoding   A(A->T)A    0

I would really appreciate your prompt help