Category:Bioinformatics

A

• Add polyphen annotation to SNPs from SeattleSeqAnnotation outputs user Kantale
• Align VCF to reference
• Align VCF to reference user Kantale
• Allele frequencies from VCF user Kantale
• Allelic R2 from minimac probs user Kantale
• Analyze beagle imputation Marchini user Kantale
• Analyze VCF diff filename user Kantale
• Annotatae variant list file via SeattleSeqAnnotation user Kantale
• Annotate list of chromosome position files with GO from BioMart Ensembl user Kantale
• Annotate variant list file via SeattleSeqAnnotation user Kantale
• Annotate VCF file via ANNOVAR user Kantale
• Annotate VCF file with GO user Kantale
• Annotate VCF file with GO user Test
• Annotate VCF filename via ANNOVAR user Kantale
• Annotate VCF filename with GO user Kantale
• ANNOVAR annotation user Kantale
• ANNOVAR Annotation user Kantale
• Assembly impute2 gprobs bins user Kantale

C

• Compare 2 TriTyper datasets user Kantale
• Compare 2 VCF files user Kantale
• Compare list of VCF files per 2 user Kantale
• Compare locus user Kantale
• Compare reference with TriTyper study user Kantale
• Compute R2 from impute2 gprobs user Kantale
• Concordance between bfiles user Kantale
• Concordance between VCF and BED user Kantale
• Concordance between VCF user Kantale
• Concordance TPED user Kantale
• Convert beagle gprobs to PEDMAP beagle user Kantale
• Convert beagle markers to MAP user Kantale
• Convert beagle to impute2 reference user Kantale
• Convert beagle to PEDMAP user Kantale
• Convert beagle to VCF user Kantale
• Convert BED BIM FAM to PEDMAP user Kantale
• Convert bim to bed user Kantale
• convert dosage plink to SNPTEST gen user Kantale
• Convert from beagle to TriTyper user Kantale
• Convert from mach to impute2 user Kantale
• convert from minimac prob to plink
• convert from minimac prob to plink user Kantale
• Convert from VCF to mach user Kantale
• Convert impute2 gprobs to beagle gprobs user Kantale
• Convert impute2 gprobs to PEDMAP beagle user Kantale
• Convert impute2 to beagle user Joman
• Convert impute2 to beagle user Kantale
• Convert impute2 to PEDMAP
• Convert impute2 to PEDMAP user Kantale
• Convert impute2 to VCF user Kantale
• Convert list beagle markers to MAP user Kantale
• Convert list beagle to PEDMAP user Kantale
• Convert list impute2 to beagle user Kantale
• Convert list impute2 to PEDMAP user Kantale
• Convert list MAPs to Beagle markers user Kantale
• Convert list MAPs to DATs user Kantale
• Convert list of PEDMAP files to GEN SAMPLE user Kantale
• Convert list of PEDMAP to GEN SAMPLE user Kantale
• Convert list PEDMAP to beagle markers user Kantale
• Convert MAP to Beagle markers user Chapmanb
• Convert MAP to Beagle markers user Kantale
• Convert MAP to DAT user Kantale
• Convert PED to TFAM user Kantale
• Convert PEDDAT to beagle user Kantale

C cont.

• Convert PEDMAP to beagle markers user Kantale
• Convert PEDMAP to beagle user Kantale
• Convert PEDMAP to GEN SAMPLE user Kantale
• Convert PEDMAP to impute2 genotype user Kantale
• Convert PEDMAP to impute2 haps legend user JohnDoe
• Convert PEDMAP to impute2 haps legend user Kantale
• Convert PEDMAP to PHASE user Kantale
• Convert PEDMAP to TriTyper user Kantale
• convert PEDMAP to VCF
• Convert PEDMAP to VCF user Kantale
• convert plink to Merlin
• convert plink to Merlin user Kantale
• Convert plink to VCF user Kantale
• Convert tab file to VCF user Kantale
• Convert TAB to GFF3 user Kantale
• Convert TPED to impute2 hap legend user Kantale
• Convert TPED to VCF user Kantale
• Convert TriTyper to PEDMAP user Kantale
• Convert VCF file to TAB user Kantale
• Convert VCF from 33 to 40 user Kantale
• Convert VCF to beagle unphased trio user Kantale
• Convert VCF to beagle user Kantale
• Convert VCF to PEDMAP user Kantale
• Convert VCF to TAB user Kantale
• Create batches from TriTyper user Kantale
• Create GO annotation ffrom BioMart Ensembl user Kantale
• Create random subset of beagle user Kantale
• Create random subset of impute2 user Kantale
• Create samples from impute2 gprobs user Kantale

D

• Default VCF header user Kantale
• Divide PEDMAP to chromosome user Kantale
• Divide PEDMAP to chromosomes user Kantale
• Dosage hap legend user Kantale

F

• From impute2 to beagle user Kantale

G

• Genetic liftover user Kantale
• Get length of chromosomes build36 user Kantale
• Get length of chromosomes build37 user Kantale
• Get polyphen annotation from SeattleSeqAnnotation with priority duplicate resolution user Kantale
• Get positions from MAP File user Kantale
• Get rsIDs from MAP File user Kantale
• Get sample names from vcf user Kantale
• Get SNP alleles user Kantale

H

• Hardy Weinberg Equilibrium asymptotic test
• Hardy Weinberg Equilibrium asymptotic test user Kantale
• Hardy Weinberg Equilibrium exact test
• Hardy Weinberg Equilibrium exact test user Kantale

I

• imputation allele frequency
• imputation allele frequency dosage
• imputation allele frequency dosage user Kantale
• Imputation allele frequency user Kantale
• imputation allelic R2
• Imputation Allelic R2 user Kantale
• Imputation pipeline impute2 user Joman
• Imputation pipeline user Joman
• Imputation pipeline user Kantale
• imputation r square hat
• imputation real allelic R2
• Imputation real allelic R2 user Kantale
• Impute BED BIM FAM files with one phased reference panel with impute2 user Kantale
• Impute PEDMAP files with impute2 user Kantale
• Impute PEDMAP vs impute2 with beagle user Kantale
• Impute TriTyper files with beagle user Kantale

I cont.

• Impute with beagle user Kantale
• impute2 info
• impute2 info user Kantale
• Impute2 with one phased reference panel user Kantale
• Install vcftools user Kantale

K

• king sample data
• king sample data user Kantale

L

• Length of chromosomes build 36
• Length of chromosomes build 37
• LiftOver TAB pipeline user Kantale
• LiftOver TPED pipeline user Kantale
• Liftover VCF user Kantale
• load PEDMAP
• Load PEDMAP user Kantale

M

• Merge beagle datasets user Kantale
• Merge beagle datasets vertically user Kantale
• Merge beagle markers user Kantale
• Merge TPED files user Kantale
• minimac info sample data
• minimac prob sample data
• minimac rsq
• minimac rsq user Kantale
• Minor allele frequency
• Minor allele frequency user Kantale

N

• Normalize beagle datasets user Kantale

P

• Pairwise linkage disequilibrium
• Pairwise linkage disequilibrium user Antonakd
• Pairwise linkage disequilibrium user Kantale
• parse king kin
• parse king kin user Kantale
• plink dosage info user Kantale
• plink PED MAP sample data
• plink PED MAP sample data user Kantale
• Prepare beagle file for imputation user Kantale
• Prepare GFF from BGI for SeattleSeqAnnotation user Kantale
• Pubmed entries user Kantale

R

• r square hat user Kantale
• R square imputation quality metric
• R square imputation quality metric dosage
• R square imputation quality metric dosage user Kantale
• R square imputation quality metric user Kantale
• Random split PEDMAP user Kantale
• Remove duplicate markers from BED user Kantale
• Remove duplicates from VCF user Kantale

S

• Sequence annotation pipeline user Kantale
• SNP alleles
• SNP concordance user Kantale
• SNPTEST gen data user Kantale
• SNPTEST sample data user Kantale
• Sort tabular file according to genomic position user Kantale
• Sort VCF user Kantale
• Split TriTyper to chromosomes user Kantale
• Standardized allele frequency error user Kantale
• Statistics of imputation results user Kantale
• Substitute VCF Header user Kantale

T

• TAB allele frequencies from VCF user Kantale

U

• Use impute2 with one phased reference panel for complete chromosome in batches user Kantale

V

• VCF sample
• VCF sample user Kantale
• VCF version user Kantale