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Revision as of 21:46, 18 June 2014
, 21:46, 18 June 2014→Step 0: vcf --> geno
== Preparing input files for LASER ==
== Preparing input files for LASER ==
= Step 0: vcf --> geno =
=== Step 0: vcf --> geno ===
This step prepares the reference panel by converting a VCF genotype file to a GENO file. We will skip this step and use a ready-to-use HGDP reference panel. A typical command to run the vcf2geno tool is given in the file "./LASER-2.01/vcf2geno/cmd.sh":
This step prepares the reference panel by converting a VCF genotype file to a GENO file. We will skip this step and use a ready-to-use HGDP reference panel. A typical command to run the vcf2geno tool is given in the file "./LASER-2.01/vcf2geno/cmd.sh":
Step 1: bam --> pileup
=== Step 1: bam --> pileup ===
This step uses samtools to generate pileup files from bam files.
This step uses samtools to generate pileup files from bam files.
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > 121101861.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > 121101861.recal.pileup &
Step 2: pileup --> seq
=== Step 2: pileup --> seq ===
In this step, we will generate a file called "hapmap_trios.seq", containing the information of 6 samples. It takes about 30 seconds to run.
In this step, we will generate a file called "hapmap_trios.seq", containing the information of 6 samples. It takes about 30 seconds to run.
== Estimating ancestry coordinates ==
== Estimating ancestry coordinates ==
Step 0: Generate the reference ancestry space (using the PCA mode of the LASER program)
=== Step 0: Generate the reference ancestry space ===
LASER can perform principal components analysis (PCA) on genotype data of the reference panel to generate a reference ancestry space.
# ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
# ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
less -S $HGDP/HGDP_938.RefPC.coord
less -S $HGDP/HGDP_938.RefPC.coord
Step 1: Place sequenced samples into the reference ancestry space:
=== Step 1: Estimate ancestry for sequenced samples ===
Submit two jobs to place sequenced samples into the reference ancestry space:
./LASER-2.01/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapmap_trios.1-3 &
./LASER-2.01/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapmap_trios.1-3 &
The running time is ~10 minutes for processing 3 samples in each job.
The running time is ~10 minutes for processing 3 samples in each job.
Step 2: Combine results
=== Step 2: Combine results ===
Results from previous step will be output to two files "hapmap_trios.1-3.SeqPC.coord" and "hapmap_trios.4-6.SeqPC.coord".
Results from previous step will be output to two files "hapmap_trios.1-3.SeqPC.coord" and "hapmap_trios.4-6.SeqPC.coord".
