Question: Verify a patient from his exome
0
gravatar for sacha
3.2 years ago by
sacha1.9k
France
sacha1.9k wrote:

I would like to know the best approch to identify a patient from his exome. For exemple I can target some locus and make the signature as follow :

  locusA: A/T 
  locusB: T/T
  locusC: GG 
  ....

But which locus ? How many ? I think I have to compute them using ExAC Allele Frequency. But It should be already done by someone ? Is there another approch ?

Thanks

id parental exome • 644 views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by sacha1.9k
2

identify is not the right word since this circles back to privacy concerns :) verify may be more appropriate.

ADD REPLYlink written 3.2 years ago by genomax78k
1
gravatar for sacha
3.2 years ago by
sacha1.9k
France
sacha1.9k wrote:

I discover this paper which seems answer to my question .

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978886/

ADD COMMENTlink written 3.2 years ago by sacha1.9k

From the paper, here are the marker . I convert as a bed file by changing position by 1

chr1    179520505   179520506
chr1    67861519    67861520
chr2    169789015   169789016
chr2    227896975   227896976
chr3    4403766 4403767
chr4    5749903 5749904
chr5    82834629    82834630
chr6    146755139   146755140
chr7    48450156    48450157
chr8    94935936    94935937
chr9    100190779   100190780
chr10   100219313   100219314
chr11   16133412    16133413
chr12   993929  993930
chr13   39433605    39433606
chr14   50769716    50769717
chr15   34528947    34528948
chr16   70303579    70303580
chr17   71197747    71197748
chr18   21413868    21413869
chr19   10267076    10267077
chr20   6100087 6100088
chr21   44323589    44323590
chr22   21141299    21141300
ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by sacha1.9k

And it works like a charm !

bedtools intersect -a exome_id_pannel.bed -b Patient.vcf.gz -loj -wb|cut -f1,2,7,8,13|cut -d":" -f1
ADD REPLYlink written 3.2 years ago by sacha1.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1308 users visited in the last hour