About delly filter -s samples.tsv

[ClarenceHsiang]

Dear delly team:

I used conda to run delly, and I face a problem in filter: The command I used as below:

delly filter -f somatic -o NK_HYNK.pre.bcf -s NK_HYNK_sample.tsv NK_HYNK.bcf

Then, it showed this error

May you give me some suggestions? Thank you

[tobiasrausch]

Looks like some problem with the sample sheet. Can you please do:

dos2unix NK_HYNK_sample.tsv

Afterwards check that the columns are okay, e.g.,

cut -f 1 NK_HYNK_sample.tsv

and

cut -f 2 NK_HYNK_sample.tsv

should give you the sample names and tumor or control.

[acarbome7]

Hello!

I am facing a similar problem... When I run:

delly filter -f somatic -o "$SV_outDir"DELLY/012_pre.bcf -s "$input_Dir"delly_sampleDescriptionFile.txt "$SV_outDir"DELLY/012.bcf

I get: "No tumor samples specified."

This is how the delly_sampleDescriptionFile.txt looks like: 012-0034-01ND control 012-02-1TD tumor

I made: dos2unix delly_sampleDescriptionFile.txt but does not work. Then I made:

cut -f 1 delly_sampleDescriptionFile.txt 012-0034-01ND 012-02-1TD

cut -f 2 delly_sampleDescriptionFile.txt control tumor

I cannot figure out what's wrong... Any other suggestions? Thank you so much for your time

[tobiasrausch]

Maybe the sample names do not match the input BCF file? Can you try:

bcftools view "$SV_outDir"DELLY/012.bcf | grep -m 1 "^#CHROM"

[NidhiAgrawal27]

Hi. Were you able to find a solution to this?

[acarbome7]

yes, I did because Delly works very well for me, but I cannot recall what was wrong. What's your question?

[NidhiAgrawal27]

Hey!

Thank you so much for responding. I solved it. In my case spelling of 'tumor' in samples.tsv was the issue. I was using 'tumour'.

Best Nidhi