merge CNV calls from different softwares
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Entering edit mode
15 months ago
Taylor95 ▴ 10

Hi all, I have used the same samples to call CNVs by three softwares, PennCNV, Birdsuite, QuantiSNP. Then, I want to get consensus CNVs called by all softwares, but don't know how to do. Would someone help me solve this? Thanks in advance!

The call format is a simple text format with one CNV call per line. An example is given below: chr3:37957465-37961253 numsnp=3 length=3,789 state2,cn=1 father.txt startsnp=rs9837352 endsnp=rs9844203 conf=15.133

chr3:75511365-75650909 numsnp=7 length=139,545 state2,cn=1 father.txt startsnp=rs4677005 endsnp=rs2004089 conf=26.862

chr11:81181640-81194909 numsnp=9 length=13,270 state2,cn=1 father.txt startsnp=rs7947005 endsnp=rs12293984 conf=35.083

chr20:10440279-10511908 numsnp=10 length=71,630 state2,cn=1 father.txt startsnp=rs8114269 endsnp=rs682562 conf=39.410

chr11:55127597-55204003 numsnp=11 length=76,407 state2,cn=1 mother.txt startsnp=rs2456022 endsnp=rs7934845 conf=23.106

CNV PennCNV Birdsuite QuantiSNP • 315 views
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Entering edit mode
15 months ago

If your variants are in VCF format, take a look at the merge subcommand of SURVIVOR .

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