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Pindel minimum deletion length

In order to reduce the pindel execution time we would like to set a minimum SV size, for example reporting only deletions larger than 50bp.

Is there a way to set such a minimum SV size when running pindel?

Thank you very much in advance for your help.

cnv
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updated by Biostar Biostar • written by thomas.faraut • thomas.faraut

1 answer

Not aware of the option when running pindel itself; however, you can control the SV size when converting to VCF via pindel2vcf with --max_size

/Programs/pindel/pindel2vcf --pindel_output_root pindelOutput/ \
-r /ReferenceMaterial/mm10/mm10.fasta -R mm10 -d 99999999 \
--min_coverage 1 --het_cutoff 0.1 --hom_cutoff 0.9 \
--max_size 10 --vcf temp.vcf

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S14T
chr4    126311485   .   TCG T   .   PASS    END=126311487;HOMLEN=1;HOMSEQ=C;SVLEN=-2;SVTYPE=DEL GT:AD   0/0:81,1
chr4    126311485   .   TCGCCCT TAGAAAA .   PASS    END=126311491;HOMLEN=0;SVLEN=-6;SVTYPE=RPL;NTLEN=6  GT:AD   0/0:83,1
chr4    126311487   .   GC  G   .   PASS    END=126311488;HOMLEN=2;HOMSEQ=CC;SVLEN=-1;SVTYPE=DEL    GT:AD   0/1:82,42
chr4    126311490   .   CT  C   .   PASS    END=126311491;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/0:83,3
chr4    126311491   .   TG  T   .   PASS    END=126311492;HOMLEN=1;HOMSEQ=G;SVLEN=-1;SVTYPE=DEL GT:AD   0/1:86,27
chr4    126311491   .   T   TTA .   PASS    END=126311491;HOMLEN=0;SVLEN=2;SVTYPE=INS   GT:AD   0/0:86,1
chr4    126311491   .   TGGAGGGCCA  TTTCTTTCCC  .   PASS    END=126311500;HOMLEN=0;SVLEN=-9;SVTYPE=RPL;NTLEN=9  GT:AD   0/0:92,1
chr4    126311493   .   GA  G   .   PASS    END=126311494;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/1:87,11
chr4    126311494   .   A   AG  .   PASS    END=126311494;HOMLEN=3;HOMSEQ=GGG;SVLEN=1;SVTYPE=INS    GT:AD   0/0:88,3
chr4    126311494   .   AG  A   .   PASS    END=126311495;HOMLEN=2;HOMSEQ=GG;SVLEN=-1;SVTYPE=DEL    GT:AD   0/1:88,71
chr4    126311497   .   GC  G   .   PASS    END=126311498;HOMLEN=1;HOMSEQ=C;SVLEN=-1;SVTYPE=DEL GT:AD   0/1:89,64
chr4    126311499   .   CA  C   .   PASS    END=126311500;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/1:92,12
chr4    126311499   .   CAG C   .   PASS    END=126311501;HOMLEN=0;SVLEN=-2;SVTYPE=DEL  GT:AD   0/0:92,1
chr4    126311499   .   CAGGGGTGGCA CCT .   PASS    END=126311509;HOMLEN=0;SVLEN=-10;SVTYPE=RPL;NTLEN=2 GT:AD   0/0:98,1

/Programs/pindel/pindel2vcf --pindel_output_root pindelOutput/ \
-r /ReferenceMaterial/mm10/mm10.fasta -R mm10 -d 99999999 \
--min_coverage 1 --het_cutoff 0.1 --hom_cutoff 0.9 \
--max_size 2 --vcf temp.vcf

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S14T
chr4    126311485   .   TCG T   .   PASS    END=126311487;HOMLEN=1;HOMSEQ=C;SVLEN=-2;SVTYPE=DEL GT:AD   0/0:81,1
chr4    126311487   .   GC  G   .   PASS    END=126311488;HOMLEN=2;HOMSEQ=CC;SVLEN=-1;SVTYPE=DEL    GT:AD   0/1:82,42
chr4    126311490   .   CT  C   .   PASS    END=126311491;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/0:83,3
chr4    126311491   .   TG  T   .   PASS    END=126311492;HOMLEN=1;HOMSEQ=G;SVLEN=-1;SVTYPE=DEL GT:AD   0/1:86,27
chr4    126311491   .   T   TTA .   PASS    END=126311491;HOMLEN=0;SVLEN=2;SVTYPE=INS   GT:AD   0/0:86,1
chr4    126311493   .   GA  G   .   PASS    END=126311494;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/1:87,11
chr4    126311494   .   A   AG  .   PASS    END=126311494;HOMLEN=3;HOMSEQ=GGG;SVLEN=1;SVTYPE=INS    GT:AD   0/0:88,3
chr4    126311494   .   AG  A   .   PASS    END=126311495;HOMLEN=2;HOMSEQ=GG;SVLEN=-1;SVTYPE=DEL    GT:AD   0/1:88,71
chr4    126311497   .   GC  G   .   PASS    END=126311498;HOMLEN=1;HOMSEQ=C;SVLEN=-1;SVTYPE=DEL GT:AD   0/1:89,64
chr4    126311499   .   CA  C   .   PASS    END=126311500;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/1:92,12
chr4    126311499   .   CAG C   .   PASS    END=126311501;HOMLEN=0;SVLEN=-2;SVTYPE=DEL  GT:AD   0/0:92,1
chr4    126311500   .   A   AG  .   PASS    END=126311500;HOMLEN=4;HOMSEQ=GGGG;SVLEN=1;SVTYPE=INS   GT:AD   0/1:92,22
chr4    126311500   .   AG  A   .   PASS    END=126311501;HOMLEN=3;HOMSEQ=GGG;SVLEN=-1;SVTYPE=DEL   GT:AD   0/1:92,82
chr4    126311504   .   GT  G   .   PASS    END=126311505;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/0:93,4
chr4    126311505   .   TG  T   .   PASS    END=126311506;HOMLEN=1;HOMSEQ=G;SVLEN=-1;SVTYPE=DEL GT:AD   0/0:94,10
chr4    126311508   .   CA  C   .   PASS    END=126311509;HOMLEN=0;SVLEN=-1;SVTYPE=DEL  GT:AD   0/1:98,26
chr4    126311508   .   CAG C   .   PASS    END=126311510;HOMLEN=0;SVLEN=-2;SVTYPE=DEL  GT:AD   0/0:99,1

There also exists --min_size

Kevin

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written by Kevin Blighe Kevin Blighe

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