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Reproducing Yang et al. - Chr1 Joint Genotyping
March 9, 2017
Reproducing Yang et al - HaplotypeCaller
March 8, 2017
Reproducing Yang et al - BQSR
March 6, 2017
download from SRA
February 28, 2017
I'm working on reproducing results from a paper using my methods.
Make bwa index of Nipponbare v7:
Turns out there are some fasta formatting mistakes in the nipponbare ref...
Prep the file for GATK:
I processed the raw reads for alignment:
And aligned (o...
December 11, 2016
I would like to run my GATK snp calling on two bam files as if they were one biological sample.
There are a two recommended ways of doing this (mentioned here), and since I have already done BQSR I have decided to try the second way.
I just need to change the read grou...
October 31, 2016
Ok so now that an alternative reference fasta is made we can align the other samples to it.
qsub bwa-v.sh -v FILE=***
and then sort and dedup the sams:
qsub picard_sort_dedup-v.sh -v REF=*****.fasta -v NAME=***_aln
October 27, 2016
Ok so once the bases have been calibrated using a bootstrapped BQSR, variants have been called on calibrated data, snps and indels filtered and combined..... we can now make the Gy_genome.fasta.
Using FastAlternativeReferenceMaker (still part of GATK).
October 17, 2016
In order to actually call SNPs vs Gy14 we need to make it an alternate reference.
Very helpful GATK ppt
Following the best practices described on the GATK tutorial here.
First step after aligning is to mark duplicate reads:
From picard help: "duplicate reads are defined a...