20 June 2014
DGE, Medicago, giraffe, and VCFNext post Previous post
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.
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…
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