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.
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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