Changes between Version 8 and Version 9 of GwasQcPipeline


Ignore:
Timestamp:
Feb 10, 2011 5:35:13 PM (11 years ago)
Author:
Morris Swertz
Comment:

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  • GwasQcPipeline

    v8 v9  
    3636Get missing data information:
    3737
    38  {{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
     38{{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
    3939 
    4040Get heterozygocity information:
     
    4545* In R:
    4646
    47 {{{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")}}}
     47{{{
     48het <- read.table("GvNL_raw_final.het", head=TRUE)
     49mis <- read.table("GvNL_raw_final.imiss", head=TRUE);
     50het$HET_RATE = (het$"N.NM." - het$"O.HOM.")/het$"N.NM."&#10;plot (mis$F_MISS,het$HET_RATE, xlab="Missing SNPs", ylab="Heterozygocity Rate")}}}
    4851
    4952No samples with callrate < 95% (Filtered in lab)
     
    5356In R:
    5457
    55 {{{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)}}}
     58{{{
     59het_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)));
     60het_fail$HET_DST = (het_fail$HET_RATE-mean(het$HET_RATE))/sd(het$HET_RATE);
     61write.table(het_fail, "fail-het-qc.txt", row.names=FALSE)}}}
    5662
    5763Result: