Genotypes

Create a personal genome

Using gtgtools to make a haploid version. Insert only the homozygous alternate SNPs/indels (ie markes as 1/1 in the VCF file).

Other tools exist to do this too, such as WASP. This makes diploid genomes, and requires phased genomes.

Mapping

See the RNA-seq alignment page.

Counting

IGVTools version

igvtools=/sonas-hs/gillis/hpc/home/sballouz/IGVTools/igvtools.jar

java -jar $igvtools count -z 0 -w 1 --bases --strands read   \
   chrX.split.filtered.bam   \
   chrX.split.filtered.wig   \
   chrX.fa

GATK

picard=/sonas-hs/gillis/hpc/home/sballouz/GenomeAnalysisTK/picard.jar
GATK=/sonas-hs/gillis/hpc/home/sballouz/GenomeAnalysisTK/GenomeAnalysisTK.jar

java -jar $GATK \
   -T ASEReadCounter \
   -R genome.fa \
   -o chrX.counts.csv \
   -I chrX.split.filtered.bam \
   -sites chrX.split.filtered.vcf \
   -U ALLOW_N_CIGAR_READS

Assessing