Delly vcf output

[Ana1335]

Hello, I am running delay on three cancer cell lines to find TVs. This is my running command (I found it is very time consuming to run all TVs together so running them separately)

for name in DEL DUP INV TRA INS; 
    do delly call -t ${name} -g ${FASTA} ${INPUT_DIR}/${SAMPLE_ID}.rmdup1.bam  > ${OUT_DIR}/${SAMPLE_ID}_${name}_delly.vcf
done

but the output vcfs I get have only these with no variants:

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2023-Dec-10 05:32:43] Split-read alignment

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2023-Dec-10 06:28:07] Junction read annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2023-Dec-10 06:47:33] Breakpoint spanning coverage annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2023-Dec-10 07:19:49] Read-depth annotation

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2023-Dec-10 08:25:23] Genotyping

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
[2023-Dec-10 08:25:25] Library statistics
Sample: RD.rmdup1

Am I doing anything wrong? Thanks

[tobiasrausch]

Probably easier to output the BCF:

delly call -o ${SAMPLE_ID}.bcf -g ${FASTA} ${INPUT_DIR}/${SAMPLE_ID}.rmdup1.bam

[Ana1335]

Thanks @tobiasrausch. Yes, it is running now but my files are so big and I am doing in a for loop, ie looping through each SV type

for name in DEL DUP INV TRA INS; 
    do delly call -t ${name} -o ${OUT_DIR}/${SAMPLE_ID}_${name}_delly.bcf -g ${FASTA} ${INPUT_DIR}/${SAMPLE_ID}.rmdup1.bam   
done

It is running since yesterday but there is no output file yet. Should I expect this? (I mean should I expect to see the output file when the run is compelete?). Thanks a lot

[tobiasrausch]

Sure, once the run is complete there should be a BCF output file for each SV type.