Changes between Version 6 and Version 7 of GwasQcPipeline

Timestamp:

Feb 10, 2011 5:32:47 PM (13 years ago)

Author:

Morris Swertz

Comment:

--

GwasQcPipeline

@@ -1 +1 @@
 = GWAS QC pipeline =
 
-Removed all bad samples (taken from Mathieu). 
+Removed all bad samples (taken from Mathieu).
+ 
 {{{p-link --bfile GvNL_250111 --remove GvNL_bad_samples.txt --make-bed --out GvNL_good_samples}}}
 
 Update family information
+
 {{{p-link --bfile GvNL_samples --update-ids GvNL_family_update.txt  --make-bed --out GvNL_good_fam}}}
 
 Set trio relationships
+
 {{{p-link --bfile GvNL_good_fam --update-parents GvNL_parents_update.txt  --make-bed --out GvNL_good_fam_par}}}
 
 Manual check for suspicious individuals (not in trios) and remove them
+
 {{{<pre>p-link --bfile GvNL_good_fam_par --remove GvNL_suspicious.txt  --make-bed --out GvNL_good_fam_par_susp}}}
 
@@ -16 +20 @@
 
 Check and update sex information
+
 {{{p-link --bfile GvNL_good_fam_par_susp --check-sex --make-bed}}}
 
@@ -24 +29 @@
 
 Update sex information for children and swapped individuals
+
 {{{<pre>p-link --bfile GvNL_good_fam_par_susp --update-sex GvNL_sex_update.txt --make-bed --out GvNL_raw_final}}}
 
 Identification 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]]
 
-Get missing data information: {{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
+Get missing data information:
+
+ {{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
  
-Get heterozygocity information: {{{p-link --bfile GvNL_raw_final --het --out GvNL_raw_final}}}
+Get heterozygocity information: 
+
+{{{p-link --bfile GvNL_raw_final --het --out GvNL_raw_final}}}
 
 Calculate 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. 
-* In R: {{{het <- read.table("GvNL_raw_final.het", head=TRUE)&#10;mis <- read.table("GvNL_raw_final.imiss", head=TRUE)&#10;het$HET_RATE = (het$"N.NM." - het$"O.HOM.")/het$"N.NM."&#10;plot (mis$F_MISS,het$HET_RATE, xlab="Missing SNPs", ylab="Heterozygocity Rate")}}}
+* In R: 
+
+{{{het <- read.table("GvNL_raw_final.het", head=TRUE)&#10;mis <- read.table("GvNL_raw_final.imiss", head=TRUE)&#10;het$HET_RATE = (het$"N.NM." - het$"O.HOM.")/het$"N.NM."&#10;plot (mis$F_MISS,het$HET_RATE, xlab="Missing SNPs", ylab="Heterozygocity Rate")}}}
 
 No samples with callrate < 95% (Filtered in lab)
@@ -39 +51 @@
 Put samples where heterozygocity rate is outside 3 standard dev from the mean (Anderson, NP2010, p.1569) in fail-het-3sd-qc.txt, along with their deviation from the mean
 
-In R: {{{het_fail = subset(het, (het$HET_RATE < mean(het$HET_RATE)-3*sd(het$HET_RATE)) | (het$HET_RATE > mean(het$HET_RATE)+3*sd(het$HET_RATE)))&#10;het_fail$HET_DST = (het_fail$HET_RATE-mean(het$HET_RATE))/sd(het$HET_RATE)&#10;write.table(het_fail, "fail-het-qc.txt", row.names=FALSE)}}}
+In R: 
+
+{{{het_fail = subset(het, (het$HET_RATE < mean(het$HET_RATE)-3*sd(het$HET_RATE)) | (het$HET_RATE > mean(het$HET_RATE)+3*sd(het$HET_RATE)))&#10;het_fail$HET_DST = (het_fail$HET_RATE-mean(het$HET_RATE))/sd(het$HET_RATE)&#10;write.table(het_fail, "fail-het-qc.txt", row.names=FALSE)}}}
 
 Result:
@@ -46 +60 @@
 Check inheritance and duplicates
 * Prune SNPs for LD
+
 {{{p-link --bfile GvNL_raw_final --indep-pairwise 50 5 0.2 --out GvNL_raw_final}}}
+
 * Generate pairwise Identity-By-State (IBS) metrics using pruned SNPs only
+
 {{{<pre>p-link --bfile GvNL_raw_final --extract GvNL_raw_final.prune.in --genome --out GvNL_raw_final}}}
+
 * 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.
 * 2 Families are not real families (G34c (child) is wrong and A56b (mother) is wrong)
 * Duplicated family: R24 == R25
+
 Check trio inheritance based on Mendelian segregation
+
 {{{p-link --file GvNL_raw_final --me 0.05 0.1 --make-bed --out GvNL_inheritance}}}