Question: Running Delly for structural Variants
0
gravatar for always_learning
3.3 years ago by
always_learning1000
Doha, Qatar
always_learning1000 wrote:

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

delly sv • 3.5k views
ADD COMMENTlink modified 3.3 years ago by trausch1.4k • written 3.3 years ago by always_learning1000
1
gravatar for trausch
3.3 years ago by
trausch1.4k
Germany
trausch1.4k wrote:

-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')

ADD COMMENTlink written 3.3 years ago by trausch1.4k

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

ADD REPLYlink written 3.3 years ago by always_learning1000

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

ADD REPLYlink written 3.3 years ago by trausch1.4k

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

ADD REPLYlink written 3.3 years ago by always_learning1000

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

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

ADD REPLYlink written 3.3 years ago by trausch1.4k
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