Showing: gatkreset
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PINDEL and somatic mutations
gatk indelrealigned pindel written 8 months ago by Leandro de Mattos80 • updated 4 days ago by Kevin Blighe24k
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153
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7 follow
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Removing Duplicates before aligning
gatk dna-seq next-gen written 5 days ago by newbinf0 • updated 4 days ago by gb210
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Why not simple Gaussian model instead of Gaussian mixture for VQSR?
vqsr gatk written 7 weeks ago by CY140 • updated 7 days ago by Biostar ♦♦ 20
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Size different between two uBam file which generate from the same Fastq.
gatk bam samtools written 12 days ago by weichi10 • updated 12 days ago by h.mon16k
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Read group information
gatk picard read group bwa written 15 days ago by bwczech0 • updated 15 days ago by WouterDeCoster30k
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GBS SNPs calling
fast-gbs gatk snp calling samtools gbs written 17 months ago by shinken12350 • updated 18 days ago by Arthur Melo0
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12 follow
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How to get sample names and genotype for SNP in multi-sample VCF file
gatk genotype snp written 5 months ago by hellbio320 • updated 22 days ago by Pierre Lindenbaum110k
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Input for VariantsToBinaryPed
gatk plink written 4 weeks ago by archie50 • updated 4 weeks ago by zx87544.7k
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152
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1
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BQSR vs VQSR
gatk snp written 5 weeks ago by James Reeve10 • updated 5 weeks ago by finswimmer3.6k
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GATK SNPs calling multiple sample without any known SNPs database
gatk multiple-sample bsqr snp written 6 weeks ago by deepkumar198340 • updated 6 weeks ago by YaGalbi1.3k
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GATK HaolotypeCaller takes too much time for variant calling
haplotypecaller gatk long written 8 months ago by J.F.Jiang700 • updated 7 weeks ago by YaGalbi1.3k
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combineVariants error for merging two vcf files
gatk combinevariants snp written 4 months ago by GK161030 • updated 8 weeks ago by Biostar ♦♦ 20
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12
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use gatk phased vcf as input file of HapCut2
hapcut2 gatk vcf phasing written 10 weeks ago by Peter Chung70 • updated 9 weeks ago by Ram16k
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148
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Calculate Depth with and without Soft-Clipping
gatk bam alignment sequencing written 9 weeks ago by ccnn0 • updated 9 weeks ago by Pierre Lindenbaum110k
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[ERROR] Malformed VCF: empty alleles are not permitted in VCF records
vcf gatk rna-seq written 2.4 years ago by umn_bist310 • updated 9 weeks ago by Biostar ♦♦ 20
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Log-odds based filtering and pairHMM alignment during local realignment
gatk mutect bayes written 4 months ago by CY140 • updated 9 weeks ago by Biostar ♦♦ 20
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Adjust ulimit open file handle limit on Mac OS X Sierra for GATK
gatk gatk3 macosx unix ulimit written 10 weeks ago by gaelgarcia05180 • updated 10 weeks ago by Alex Reynolds24k
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