Running Delly for structural Variants

Question

[always_learning]

I am running Delly commands to get SV and used these two commands .

             1. delly call -t DEL -g genome.fa -o s1.bcf S1_L001.sorted.bam
             2. delly call -g genome.fa -o s1-All.bcf S1_L001.sorted.bam

In both cases (1) and (2) , its calling "DELETION" only not other types of SV.

Can some one help me with Delly options that can call all types of SV's like DELETION, DUPLICATION etc ?

Thanks

Answer 1

[trausch]

-t DEL # Deletions

-t INS # Insertions

-t INV # Inversions (3' to 3' and 5' to 5')

-t DUP # Tandem Duplications

-t TRA # Inter-chromosomal translocations (3' to 3', 3' to 5', 5' to 3' and 5' to 5')

[always_learning]

So I have to give all options separately. Is their some options for all in one ?

[trausch]

Yes, but you can of course put them all in a simple shell script.

[always_learning]

yes That I can do off course. Any idea if you can merge all files into one as well ?

[trausch]

Sure, you can just merge (concatenate) them together:

bcftools concat -a -O b -o merged.bcf DEL.bcf INS.bcf ...