assembly of preliminary data for proposal - May 04, 2015 7:50:23 PM
variant calling with GATK - May 04, 2015 10:31:53 PM
summary of variant calling, 1st pass - May 07, 2015 10:56:54 PM
clustering to count haplotypes as a first pass at ploidy - Aug 04, 2015 3:3:37 PM
results from initial attempt at haplotype counting - Aug 04, 2015 5:11:0 PM
plans for estimating haplotypes - Aug 24, 2015 4:30:42 PM
defining hapltype loci - Aug 27, 2015 3:26:48 PM
grabbing SNPs for haplotype loci and narrowing the set down - Sep 03, 2015 3:54:46 PM
removing indels, recreating bam files, and extracting haplotype data - Sep 21, 2015 6:32:40 PM
extract genotypic data, test run - Sep 21, 2015 6:34:10 PM
discriminating between diploids and triploids - Oct 16, 2015 1:42:7 AM
variant calling for diploids and triploids - Nov 02, 2015 3:9:20 AM
variant comparison for dips and trips - Nov 10, 2015 4:43:4 AM
filtering and combining vcf files - Nov 30, 2015 4:48:59 AM
aspen vcf to genotypes - Nov 30, 2015 6:38:15 PM
overview and refinement of pipeline - Dec 14, 2015 4:41:54 AM
Processing the pando and rangewide aspen samples - Aug 22, 2018 9:8:1 PM
Filtering aspend pando plus rangewide, iteration 1 (pre ploidy calling) - Nov 19, 2018 2:14:24 AM
Aspen/Pando, low number of variants, trouble shooting - Feb 25, 2019 4:1:51 PM
Aspen/Pando, alignment with bwa mem - Oct 30, 2019 10:10:18 PM
Untitled Post - Oct 31, 2019 11:58:8 PM
Pando plus variant calling and filtering with samtools/bcftools multiallelic variant caller - Nov 05, 2019 3:7:35 AM
Pando plus, estimating allele frequencies and genotypes for the bcftools multiallelic SNPs - Nov 05, 2019 3:13:55 AM
Generating a panel of normals for MuTect2 - Nov 21, 2019 5:52:28 PM
Running MuTect2 w/o the PoN - Nov 21, 2019 6:0:0 PM
PCR duplicates and mutect2, redoing alignments - Nov 23, 2019 3:25:23 AM