I am doing CNV analysis on 250 samples on PennCNV.
What I want: make a file with Choromosome that passes my SNP density threshold in .cnv format/remove chromosome that did not pass threshold from the .cnv file.
My Scenario: I merged any CNV calls that overlap another (or several other) CNV call by a minimum of 20% of their lengths overlapped using this command.
./clean_cnv.pl combineseg --fraction 0.2 --signalfile ./lib/cohort.pfb cohort_filtered.annotated.cnv > cohort_gapmerged.cnv
So, the file is currently on CNV format. I want to check the SNP density by dividing numsnp/length. I paste the info to excel and filter according to my threshold. The problem is, once I know which chromosome didn't pass & have the list, I have to delete the chromosome one by one at the .cnv file.
I really appreciate if someone could tell me how to delete the chromosome using other tools and return it back to the original .cnv format. Or tell me other methods which is better lol
1 answer
if file1 exactly be (tab delimited with row number in second column):
chr13:32914976-32919384 1
chr13:32900191-32900291 2
chr22:19137233-19152094 3
chr4:69401231-69493479 4
chr17:44171207-44237068 5
and
file2 exactly be (tab delimited):
chr16:77201441-77224685 numsnp=10 length=23,245 state5,cn=3sample.split220startsnp=kgp5597583endsnp=kgp11117565conf=24.089
chr4:69401231-69493479 numsnp=145 length=92,249 state5,cn=3sample.split171startsnp=4:69401231_CNV_UGT2B17endsnp=rs17663945conf=118.433
chr17:41267632-41276134 numsnp=85 length=8,503 state5,cn=3sample.split207startsnp=rs8176100endsnp=rs886040902conf=29.833
chr19:1220367-1234676 numsnp=84 length=14,310 state5,cn=3sample.split90startsnp=rs567202367endsnp=19:1234676-GAconf=88.991
chr19:41385767-41385775 numsnp=6 length=9 state1,cn=0sample.split90startsnp=19:41385767_CNV_CYP2A7endsnp=19:41385775_CNV_CYP2A7_Ilmndup2conf=21.121
chr17:44171207-44237068 numsnp=14 length=65,862 state5,cn=3sample.split166startsnp=JHU_17.44171206endsnp=rs2532292conf=21.762
chr1:1266841-1269724 numsnp=27 length=2,884 state5,cn=3sample.split60startsnp=rs577691125.1endsnp=rs536836467.2conf=20.617
chr1:2381164-2389702 numsnp=14 length=8,539 state5,cn=3sample.split60startsnp=1:2381164endsnp=1:2389702conf=20.634
chr1:228497228-228612939 numsnp=71 length=115,712 state5,cn=3sample.split60startsnp=rs761649292endsnp=rs531385963.3conf=23.547
chr13:32914976-32919384 numsnp=92 length=4,409 state5,cn=3sample.split78startsnp=rs886040659endsnp=rs191253965conf=55.675
chr22:24301643-24301695 numsnp=16 length=53 state1,cn=0sample.split209startsnp=22:24301643_CNV_GSTT2B_Ilmndup1endsnp=22:24301695_CNV_GSTT2B_Ilmndup1conf=66.493
chr22:24302601-24302603 numsnp=7 length=3 state1,cn=0sample.split209startsnp=22:24302601_CNV_GSTT2Bendsnp=22:24302603_CNV_GSTT2B_Ilmndup3conf=25.047
chr22:42522134-42522313 numsnp=12 length=180 state1,cn=0sample.split209startsnp=22:42522134_CNV_CYP2D6endsnp=22:42522313_CNV_CYP2D6_Ilmndup2conf=43.298
chr13:32900191-32900291 numsnp=31 length=101 state5,cn=3sample.split147startsnp=rs81002842endsnp=rs276174848conf=25.818
chr13:32903511-32906684 numsnp=101 length=3,174 state5,cn=3sample.split147startsnp=rs61948377endsnp=rs886040343conf=49.625
chr13:32913339-32913896 numsnp=122 length=558 state5,cn=3sample.split147startsnp=rs398122786endsnp=rs80358763conf=65.213
chr13:32914891-32921037 numsnp=153 length=6,147 state5,cn=3sample.split147startsnp=rs80359581endsnp=rs876661201conf=143.004
chr22:19137233-19152094 numsnp=13 length=14,862 state2,cn=1sample.split26startsnp=rs540621015endsnp=kgp5062455conf=20.778
chr22:24301643-24302227 numsnp=36 length=585 state5,cn=3sample.split26startsnp=22:24301643_CNV_GSTT2B_Ilmndup1endsnp=22:24302227_CNV_GSTT2B_Ilmndup1conf=35.287
chr22:24374342-24386612 numsnp=126 length=12,271 state1,cn=0sample.split26startsnp=22:24374342_CNV_GSTT1endsnp=22:24386612_CNV_GSTT1conf=317.105
This command probably works:
awk '{str=substr($0,1,index($0,"\t"))} FNR==NR{a[str];next} (str in a)' file1 file2
result:
chr4:69401231-69493479 numsnp=145 length=92,249 state5,cn=3sample.split171startsnp=4:69401231_CNV_UGT2B17endsnp=rs17663945conf=118.433
chr17:44171207-44237068 numsnp=14 length=65,862 state5,cn=3sample.split166startsnp=JHU_17.44171206endsnp=rs2532292conf=21.762
chr13:32914976-32919384 numsnp=92 length=4,409 state5,cn=3sample.split78startsnp=rs886040659endsnp=rs191253965conf=55.675
chr13:32900191-32900291 numsnp=31 length=101 state5,cn=3sample.split147startsnp=rs81002842endsnp=rs276174848conf=25.818
chr22:19137233-19152094 numsnp=13 length=14,862 state2,cn=1sample.split26startsnp=rs540621015endsnp=kgp5062455conf=20.778
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Hi, For better help, if possible, paste the output of the following commands
bash(linux):
"head -n 20 ./yourfile.cnv"powershell(win) :
"type .\yourfile.cnv | select -First 20"If I understand correctly, you want to delete the rows of the this file based on a list of "chr:start:end" similar to the first column of this file?
Yes. Thank you for replying by the way.
This is exactly what you want: https://stackoverflow.com/questions/35728766/awk-to-filter-file-by-specific-field-in-another
I tried using the code suggested by the karakfa in the website.
awk 'NR==FNR{a[$1];next} FNR==1 || ($7 in a)' file1 file2
So, I changed, the file1 = file containing the desired list file2 = file containing all the chromosome
Do I need to change other things? because it doesn't seem to work.