which one is PennCNV v2010May01 ?

[QidiFeng]

Hi Kai,

I am trying to use the same PennCNV version with a previously published paper in order to make the cnv results more comparable? The PennCNV used in that paper is PennCNV v2010May01. I am not sure which version is this? Is this PennCNV v1.0.0?

Happy new year!

Best regards, Qidi Feng

[kaichop]

PennCNV is not in github around 2010 (This is not v1.0.0). I do not have a copy of the 2010 version at hand; however, I believe that very minimal changes are made to PennCNV CNV calling procedure itself (most changes are for accessary programs, and for processing outputs or for increasing compatibility with non-human species). I think you can just use the latest version to do CNV calling.

On Fri, Jan 1, 2021 at 11:18 AM Qidi Feng notifications@github.com wrote:

Hi Kai,

I am trying to use the same PennCNV version with a previously published paper in order to make the cnv results more comparable? The PennCNV used in that paper is PennCNV v2010May01. I am not sure which version is this? Is this PennCNV v1.0.0?

Happy new year!

Best regards, Qidi Feng

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/64, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OETC4OKB7KGZQWUSBLSXXYTZANCNFSM4VQLXVFQ .

[QidiFeng]

Hi Kai,

Thank you very much for your reply! But now I got problems repeating previous paper's calling results with almost the same pipeline. Would you pls give me any hints?

The previous paper claims that they use "“hhall.hmm”, compile pfb from the data, use gcmodel adjustment, using an older version of PennCNV v2010May01". I connected with the author and got their inputs of 100 samples (containing BAF and LRR), I run PennCNVv1.0.5 with command "perl detect_cnv.pl -test -hmm ../PennCNV-1.0.5/lib/hhall.hmm -pfb taiwan100.pfb -gcmodel taiwan100.gc2 -listfile samplelist.txt -log rawcnv.log -out taiwan100.rawcnv". I compared their raw cnv results with mine, and found there are big differences in number of CNVs for some specific samples (for example 9464294022_R03C01). You may like to check detailed results between the two versions of results in the attached file.

The only difference in pipeline I can think of is 1. pfb file (I compiled pfb file from the 100 samples while the previous paper should compile pfb file from the original ~5000 samples) and 2. PennCNV version. Do you have any suggestions explaining the differences on cnv results? Do you think PFB file could potentially cause this difference?

Thanks again for your help! Happy new year!

Best, Qidi

On Sat, Jan 2, 2021 at 12:13 AM Kai Wang notifications@github.com wrote:

PennCNV is not in github around 2010 (This is not v1.0.0). I do not have a copy of the 2010 version at hand; however, I believe that very minimal changes are made to PennCNV CNV calling procedure itself (most changes are for accessary programs, and for processing outputs or for increasing compatibility with non-human species). I think you can just use the latest version to do CNV calling.

On Fri, Jan 1, 2021 at 11:18 AM Qidi Feng notifications@github.com wrote:

Hi Kai,

I am trying to use the same PennCNV version with a previously published paper in order to make the cnv results more comparable? The PennCNV used in that paper is PennCNV v2010May01. I am not sure which version is this? Is this PennCNV v1.0.0?

Happy new year!

Best regards, Qidi Feng

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/64, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNG3OETC4OKB7KGZQWUSBLSXXYTZANCNFSM4VQLXVFQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/64#issuecomment-753433129, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJ6PSOGY7MLVNYH6O5YRNVTSX2TPDANCNFSM4VQLXVFQ .

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[kaichop]

Generally you need to compile PFB from at least 100 samples, the more the better. You may want to request the original PFB files to re-generate results. Additionally, the LOG message should tell you how many markers are used in the calculation, since it is possible that only a fraction of markers in your input files are actually used (based on PFB file). Not sure what is the gcmodel file that you used, but it is usually not needed to use a gcmodel unless there are clear problems with the LRR calculation (large WF values). I do not think the version of PennCNV itself can change results much, and the hhall.hmm has not changed either.

On Sat, Jan 2, 2021 at 11:42 AM Qidi Feng notifications@github.com wrote:

Hi Kai,

Thank you very much for your reply! But now I got problems repeating previous paper's calling results with almost the same pipeline. Would you pls give me any hints?

The previous paper claims that they use "“hhall.hmm”, compile pfb from the data, use gcmodel adjustment, using an older version of PennCNV v2010May01". I connected with the author and got their inputs of 100 samples (containing BAF and LRR), I run PennCNVv1.0.5 with command "perl detect_cnv.pl -test -hmm ../PennCNV-1.0.5/lib/hhall.hmm -pfb taiwan100.pfb -gcmodel taiwan100.gc2 -listfile samplelist.txt -log rawcnv.log -out taiwan100.rawcnv". I compared their raw cnv results with mine, and found there are big differences in number of CNVs for some specific samples (for example 9464294022_R03C01). You may like to check detailed results between the two versions of results in the attached file.

The only difference in pipeline I can think of is 1. pfb file (I compiled pfb file from the 100 samples while the previous paper should compile pfb file from the original ~5000 samples) and 2. PennCNV version. Do you have any suggestions explaining the differences on cnv results? Do you think PFB file could potentially cause this difference?

Thanks again for your help! Happy new year!

Best, Qidi

On Sat, Jan 2, 2021 at 12:13 AM Kai Wang notifications@github.com wrote:

PennCNV is not in github around 2010 (This is not v1.0.0). I do not have a copy of the 2010 version at hand; however, I believe that very minimal changes are made to PennCNV CNV calling procedure itself (most changes are for accessary programs, and for processing outputs or for increasing compatibility with non-human species). I think you can just use the latest version to do CNV calling.

On Fri, Jan 1, 2021 at 11:18 AM Qidi Feng notifications@github.com wrote:

Hi Kai,

I am trying to use the same PennCNV version with a previously published paper in order to make the cnv results more comparable? The PennCNV used in that paper is PennCNV v2010May01. I am not sure which version is this? Is this PennCNV v1.0.0?

Happy new year!

Best regards, Qidi Feng

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state5,cn=3 9464294016_R05C02 startsnp=rs4827306 endsnp=snv-rs112794456 conf=4.375 chrX:149005063-149013963 numsnp=8 length=8,901 state5,cn=3 9464294016_R05C02 startsnp=rs2166782 endsnp=exm1661492 conf=3.655 chrX:153037394-153041544 numsnp=13 length=4,151 state5,cn=3 9464294016_R05C02 startsnp=exm1664088 endsnp=rs5987155 conf=9.654 chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 9464294016_R07C02 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=9.060 chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 9464294016_R07C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=8.197 chr8:39284717-39321992 numsnp=4 length=37,276 state1,cn=0 9464294016_R07C02 startsnp=psy_rs7827037 endsnp=psy_rs28851014 conf=21.822 chr2:225244304-225244923 numsnp=5 length=620 state2,cn=1 9464294016_R07C02 startsnp=variant.65840 endsnp=rs3738953 conf=19.671 chr5:139931607-139931656 numsnp=21 length=50 state2,cn=1 9464294016_R07C02 startsnp=exm482409 endsnp=exm482450 conf=36.081 chr8:24207409-24207472 numsnp=5 length=64 state2,cn=1 9464294016_R07C02 startsnp=exm690047 endsnp=exm690053 conf=19.841 chr9:11976830-11996831 numsnp=3 length=20,002 state2,cn=1 9464294016_R07C02 startsnp=rs16928298 endsnp=rs4512479 conf=12.814 chr16:72089740-72108264 numsnp=13 length=18,525 state2,cn=1 9464294016_R07C02 startsnp=rs2070937 endsnp=exm1256782 conf=14.001 chr19:20596024-20716939 numsnp=11 length=120,916 state2,cn=1 9464294016_R07C02 startsnp=psy_rs6511102 endsnp=psy_rs78893254 conf=26.229 chr1:1222596-1249194 numsnp=64 length=26,599 state5,cn=3 9464294016_R07C02 startsnp=exm2135 endsnp=indel.166 conf=30.720 chr1:3389703-3416502 numsnp=38 length=26,800 state5,cn=3 9464294016_R07C02 startsnp=exm6750 endsnp=psy_rs41307852 conf=29.808 chr2:98235080-98242427 numsnp=4 length=7,348 state5,cn=3 9464294016_R07C02 startsnp=psy_rs2692943 endsnp=kgp1336864 conf=14.091 chr2:239038829-239040270 numsnp=16 length

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