yashcrux
commented
5 months ago Hello Nidhi
I was just having a look at the your issue. I also faced something similar and dos2unix helped with it!.
In your case I can see that there is typo. It should be "tumor" in delly_samples.tsv. I think it will solve it.
NidhiAgrawal27
Hello,
I am using Delly version: v1.2.6 on Ubuntu.
I ran the following command for somatic SV calling:
TUM_BAM=../data/bam_vcf_files/tumour/orig/tumour.bam NORM_BAM=../data/bam_vcf_files/control/orig/control.bam OUT_FILE=../data/bam_vcf_files/sv_vcf/delly_conda_output.bcf HG38_EXCL=../data/hg38/human.hg38.excl.tsv CORES=8 REF=../data/GRCh83_d1_vd1/GRCh38.d1.vd1.fa delly call -x $HG38_EXCL -o $OUT_FILE -g $REF $TUM_BAM $NORM_BAM
It generated output files delly_conda_output.bcf and delly_conda_output.bcf.csi
The header in delly_conda_output.bcf file is:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TCGA-A2-A0YL-01A-21D-A744-36 TCGA-A2-A0YL-10A-01D-A723-36
My delly_samples.tsv file looks like (tab delimited): TCGA-A2-A0YL-01A-21D-A744-36 tumour TCGA-A2-A0YL-10A-01D-A723-36 control
I did dos2unix delly_samples.tsv to convert it to unix format.
Now I am running Somatic pre-filtering with command: IN_FILE=../data/bam_vcf_files/sv_vcf/delly_conda_output.bcf OUT_FILE=../data/bam_vcf_files/sv_vcf/delly.pre.bcf SAMP_TSV=delly_samples.tsv REF=../data/GRCh83_d1_vd1/GRCh38.d1.vd1.fa
delly filter -f somatic -o $OUT_FILE -s $SAMP_TSV $IN_FILE
It gave me error: Sample type for TCGA-A2-A0YL-01A-21D-A744-36 is neither tumor nor control
I also tried following command as suggested by you in another similar issue: delly filter -f somatic -o $OUT_FILE -s $SAMP_TSV -g $REF -m 0 -a 0.05 -r 0.1 $IN_FILE
This gave me error: terminate called after throwing an instance of 'boost::wrapexcept'
what(): unrecognised option '-g'
/var/spool/slurm/job3785860/slurm_script: line 19: 738313 Aborted (core dumped) delly filter -f somatic -o $OUT_FILE -s $SAMP_TSV -g $REF -m 0 -a 0.05 -r 0.1 $IN_FILE
Kindly help me resolve this issue.
Thank you in advance!
Best Nidhi