Bioinfo - Misc

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[bioinfomisc]

Error: More than 100 obvious strand flips have been detected. Please check strand. Imputation cannot be started!

Statistics: Alternative allele frequency > 0.5 sites: 0 Reference Overlap: 99.80% Match: 426,485 Allele switch: 66,772 Strand flip: 23,263 Strand flip and allele switch: 13,805 A/T, C/G genotypes: 642 Filtered sites: Filter flag set: 0 Invalid alleles: 0 Duplicated sites: 286 NonSNP sites: 0 Monomorphic sites: 0 Allele mismatch: 465 SNPs call rate < 90%: 0

beagle provided a java tool called conform-gt https://faculty.washington.edu/browning/conform-gt.html

a program for making alleles in a VCF file to be consistent with a reference VCF file, see an example:

java -jar conform-gt.24May16.cee.jar gt=input.vcf.gz chrom=$i ref=chr22.1kg.phase3.v5a.EUR.vcf.gz out=output.chr22.beagle.vcf.gz

[bioinfomisc]

On considering the .bim files at these problem snps for each population example allele codes are as follows:

Pop1: rs1000000  A  G

Pop2: rs1000000  T  C

Pop3: rs1000000  A  G

This indicates to me that Pop2 has undergone strand flip.

PLINK gives you a list of SNPs who need to be flipped (???.missnp). You need to flip these SNPs :

Step 1 - First merge: plink --file fA --merge-list allfiles.txt --make-bed --out mynewdata

Step 2 - Flip SNPs: plink --file fA --flip mynewdata.missnp --make-bed --out mynewdata2

Step 3 - New merge: plink --bfile mynewdata2 --merge-list allfiles.txt --make-bed --out mynewdata3

After the second merge, if you still have a bug about the strand, those SNPs are probably triallelic.

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MARTIN KRZYWINSKI

CANADA’S MICHAEL SMITH GENOME SCIENCES CENTER

BC CANCER RESEARCH CENTER

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Ricco Rakotomalala

Étude des dépendances - Variables qualitatives

Tableau de contingence et mesures d'association

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knitr

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- checking how much memory an object is taking; - the memory limit of 32-bit R and 64-bit R; - package designed to store objects on hard drives rather than RAM; - memory garbage collection with gc(); and - some tips to reduce memory fragmentation.

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(via Kaplan-Meier Survival Plot – with at risk table « Matt's Stats n stuff)

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(via The four steps to publication-grade graphics in R | Sustainable Research)

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Engineering Data Analysis (with R and ggplot2) (by GoogleTechTalks)

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(via Visualization Meetup at the Googleplex - Google Open Source Blog)

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(via Print Friendly & PDF)