Monday July 28 notes

ApGxL

Started DGE!

Pre-SPIA protocol done in Agnarsson lab. Washed all surfaces and lab tools with bleach. New tips, etc.

4 samples to start. Stopped after SPIA protocol. Samples in -20°C. Took 2ul aliquot for qPCR.

Medicago

For MtGIRAFFE project, need to extract SNPs for giraffe gene. Started this a few week’s ago but ran into problem with wrong SNPs recorded. Not surprising, this was a simple error due to missing a digit when specifying the SNP range: 677902-6783193 instead of 6779092-6783193.

When corrected the SNP extraction

bcftools query -H -r chr8:6779092-6783193 -f "%CHROM\t%POS[\t%TGT]\n" chr8-filtered-set-2014Apr15.bcf > Medtr8g_GIRAFFE.txt

gave 345 SNPs, all within correct range!

Can extract to VCF format with this command:

bcftools view -f PASS -r chr8:6779092-6783193 -O v -o test.vcf chr8-filtered-set-2014Apr15.bcf

Next - infer haplotypes from SNP data. The major problem of bioinformatics - every program has it’s own input. Some options and my success with them…

fastPHASE. google-fu found script to convert vcf2fastPHASE.pl. Tried to use script, but asks for “positions file”?
BEAGLE - has utility program vcf2beagle.jar to convert VCF to BEAGLE format
MACH