Changes between Version 9 and Version 10 of GwasQcPipeline


Ignore:
Timestamp:
Feb 10, 2011 5:36:17 PM (11 years ago)
Author:
Morris Swertz
Comment:

--

Legend:

Unmodified
Added
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Modified
  • GwasQcPipeline

    v9 v10  
    33Removed all bad samples (taken from Mathieu).
    44
    5 {{{p-link --bfile GvNL_250111 --remove GvNL_bad_samples.txt --make-bed --out GvNL_good_samples}}}
     5{{{
     6p-link --bfile GvNL_250111 --remove GvNL_bad_samples.txt --make-bed --out GvNL_good_samples}}}
    67
    78Update family information
    89
    9 {{{p-link --bfile GvNL_samples --update-ids GvNL_family_update.txt  --make-bed --out GvNL_good_fam}}}
     10{{{
     11p-link --bfile GvNL_samples --update-ids GvNL_family_update.txt  --make-bed --out GvNL_good_fam}}}
    1012
    1113Set trio relationships
    1214
    13 {{{p-link --bfile GvNL_good_fam --update-parents GvNL_parents_update.txt  --make-bed --out GvNL_good_fam_par}}}
     15{{{
     16p-link --bfile GvNL_good_fam --update-parents GvNL_parents_update.txt  --make-bed --out GvNL_good_fam_par}}}
    1417
    1518Manual check for suspicious individuals (not in trios) and remove them
    1619
    17 {{{<pre>p-link --bfile GvNL_good_fam_par --remove GvNL_suspicious.txt  --make-bed --out GvNL_good_fam_par_susp}}}
     20{{{
     21p-link --bfile GvNL_good_fam_par --remove GvNL_suspicious.txt  --make-bed --out GvNL_good_fam_par_susp}}}
    1822
    1923NB: After checking suspicious individuals with Mathieu, turns out it was 1 typo and 1 filtered low call rate (93%). Therefore, only the low callrate individual was screened out after all.
     
    2125Check and update sex information
    2226
    23 {{{p-link --bfile GvNL_good_fam_par_susp --check-sex --make-bed}}}
     27{{{
     28p-link --bfile GvNL_good_fam_par_susp --check-sex --make-bed}}}
    2429
    2530Crosscheck with information from Genome Studio provided by Mathieu
     
    3035Update sex information for children and swapped individuals
    3136
    32 {{{<pre>p-link --bfile GvNL_good_fam_par_susp --update-sex GvNL_sex_update.txt --make-bed --out GvNL_raw_final}}}
     37{{{
     38p-link --bfile GvNL_good_fam_par_susp --update-sex GvNL_sex_update.txt --make-bed --out GvNL_raw_final}}}
    3339
    3440Identification of individuals with elevated missing data rates or outlying heterozygosity rate (See Anderson, NP2010, p.1569) => How does this compare with the PLINK suggested approach  [[http://pngu.mgh.harvard.edu/~purcell/plink/thresh.shtml here]]
     
    3642Get missing data information:
    3743
    38 {{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
     44{{{
     45p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
    3946 
    4047Get heterozygocity information:
    4148
    42 {{{p-link --bfile GvNL_raw_final --het --out GvNL_raw_final}}}
     49{{{
     50p-link --bfile GvNL_raw_final --het --out GvNL_raw_final}}}
    4351
    4452Calculate the observed heterozygosity rate per individual using the formula (N(NM)  −  O(Hom))/N(NM) and plot the missing SNPs vs heterozygocity rate for eyeball inspection.
     
    6775* Prune SNPs for LD
    6876
    69 {{{p-link --bfile GvNL_raw_final --indep-pairwise 50 5 0.2 --out GvNL_raw_final}}}
     77{{{
     78p-link --bfile GvNL_raw_final --indep-pairwise 50 5 0.2 --out GvNL_raw_final}}}
    7079
    7180* Generate pairwise Identity-By-State (IBS) metrics using pruned SNPs only
    7281
    73 {{{<pre>p-link --bfile GvNL_raw_final --extract GvNL_raw_final.prune.in --genome --out GvNL_raw_final}}}
     82{{{
     83p-link --bfile GvNL_raw_final --extract GvNL_raw_final.prune.in --genome --out GvNL_raw_final}}}
    7484
    7585* Check trio inheritance based on IBS: Check the Pi_HAT value for the individuals (unrelated individuals =~ 0, parent <-> child =~ 0.5, siblings =~0.5, twins =~ 1.0). Done with homemade perl script.
     
    7989Check trio inheritance based on Mendelian segregation
    8090
    81 {{{p-link --file GvNL_raw_final --me 0.05 0.1 --make-bed --out GvNL_inheritance}}}
     91{{{
     92p-link --file GvNL_raw_final --me 0.05 0.1 --make-bed --out GvNL_inheritance}}}
    8293
    8394A diff between GvNL_raw_final.fam and GvNL_inheritance.fam confirms IBS version: families G34 and A56 have been removed.