TestConcordance.pl

[Thanujay Suthahar]

Hello sir,

Can you please in detail give an example on the TestConcordance.pl usage? 

I see this is the usage of the function :

perl TestConcordance.pl ArrayVsExomeXHMMCalls.txt Omni_1_2.5_NimblegenExomeXHMMCalledTargets.map

Thank you in advance

Regards,

Thanujay Suthahar

[Joe Glessner]

Hi Thanujay,

perl TestConcordance.pl ArrayVsExomeXHMMCalls.txt Omni_1_2.5_NimblegenExomeXHMMCalledTargets.map

where for example TestConcordance.pl ArrayVsExomeXHMMCalls.txt looks like:

chr1:1-3  numsnp=3 length=3  state1,cn=0 1_A.baflrr startsnp=rs1 endsnp=rs3 conf=10 Array
chr1:5-7  numsnp=3 length=3  state5,cn=3 1_A.baflrr startsnp=rs5 endsnp=rs7 conf=20 Array
chr1:1-3  numsnp=3 length=3  state1,cn=0 1_A.baflrr startsnp=rs1 endsnp=rs3 conf=15 Exome
chr1:5-7  numsnp=3 length=3  state5,cn=3 1_A.baflrr startsnp=rs5 endsnp=rs7 conf=24 Exome

and Omni_1_2.5_NimblegenExomeXHMMCalledTargets.map looks like:

Chr     Snp     Cm      Pos
1       rs1     0       1
1       rs2     0       2
1       rs3     0       3
1       rs4     0       4
1       rs5     0       5
1       rs6     0       6
1       rs7     0       7
1       rs8     0       8
1       rs9     0       9
1       rs10    0       10

ArrayVsExomeCalls.rawcnvMissingSNPs.txt - a list of SNPs in case any are missing from the map input
ArrayVsExomeCalls.rawcnvCallsMatching.txt - a list of calls in the second set (Exome calls in this case) and their hit rate with the first set (Array calls in this case)
ArrayVsExomeCalls.rawcnvCNVMatchSummary.txt - a list per sample of concordance between all calls

I hope this helps,

Joe Glessner

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