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<prev • 627 results • page 1 of 21 • next >
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When to remove duplicates using deduplication in Exome-Seq
trueseq dna-seq exome-seq truseq gatk written 8 hours ago by oriolebaltimore • 60 • updated 8 hours ago by Charles Warden ♦ 5.9k
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0
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114
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0
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VCFParseError: ploidy > 2 not supported
vcf gatk ploidy written 15 days ago by always_learning • 930
3
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0
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198
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0
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ERROR MESSAGE: QD annotation at VariantRecalibrator
gatk variantrecalibrator snp written 4 weeks ago by Satyajeet Khare • 1.3k • updated 4 weeks ago by Vijay Lakhujani ♦ 3.5k
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1.3k
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0
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GATK DP filter for multiple samples
gatk snps written 2.4 years ago by sun.nation • 120 • updated 4 weeks ago by Flávia Rogério • 0
0
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1
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107
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1
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Consensus VCF file from several variant callers
vcf variant calling freebayes gatk written 4 weeks ago by ajuiwl • 30 • updated 4 weeks ago by Pierre Lindenbaum ♦ 116k
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0
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70
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Effect of dbSNP build differences in variant calling
assembly grch38 dbsnp variantcalling gatk written 5 weeks ago by Mehulsharma.253 • 10
6
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2
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152
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2
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Bash vs WDL for running GATK
gatk cromwell pipeline linux wdl written 6 weeks ago by Mehulsharma.253 • 10 • updated 5 weeks ago by vdauwera • 890
1
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1
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146
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1
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Warning in GATK Picard MarkDuplicates
variant calling gatk picard markduplicates written 5 weeks ago by Mehulsharma.253 • 10 • updated 5 weeks ago by Pierre Lindenbaum ♦ 116k
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0
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138
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0
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Stop GATK MergeBamAlignment from unmapping reads
gatk4 gatk alignment bam mergebamalignment written 5 weeks ago by ttmigueltt • 0 • updated 5 weeks ago by finswimmer ♦ 8.8k
2
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1
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985
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1
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GATK: -nct and -nt
gatk parallel written 21 months ago by fire_water • 80 • updated 5 weeks ago by nick.carleson • 10
3
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1
answer
168
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1
answer
Issues with Marking Duplicates in Picard
gatk picard samtools sorting bwa written 6 weeks ago by sarah.kettelkamp • 0 • updated 6 weeks ago by goodez • 420
1
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0
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163
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5 follow
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picard addorreplacereadgroups output issue
gatk readgroups picard java sequencing written 6 weeks ago by Peter Chung • 70
1
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1
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127
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1
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gatk HaplotyperCaller bam reference
haplotypercaller gatk bam written 6 weeks ago by Peter Chung • 70
1
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1
answer
269
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1
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How can I find SNPs between two Genomes?
genome gatk snp fasta written 7 weeks ago by Zeason • 0 • updated 7 weeks ago by zx8754 ♦ 6.2k
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177
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0
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How can I find Variants position by GATK and Samtools
gatk samtools snp written 10 weeks ago by Mbillah • 100 • updated 8 weeks ago by Biostar ♦♦ 20
0
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0
answers
180
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0
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algorithm of gatk re-alignment
gatk realignment algorithm re-alignment written 9 weeks ago by lffu_0032 • 30
1
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0
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197
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0
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Standard Practice of making VCF file from SAM file
gatk snp written 10 weeks ago by hafiz.talhamalik • 40 • updated 9 weeks ago by Biostar ♦♦ 20
2
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1
answer
186
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1
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Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
haplotypecaller gatk written 10 weeks ago by Nandini • 750 • updated 9 weeks ago by lffu_0032 • 30
3
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0
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134
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0
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Same pipeline for exome seq variant calling with different results
bwa-mem fastp snp gatk written 10 weeks ago by paumarc • 10
2
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0
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158
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0
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Needed gatk latest version pipline for variant calling
gatk written 10 weeks ago by Mbillah • 100
0
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1
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180
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1
answer
GATK Panel Of Normals (PoN)
gatk beta calling variant written 11 weeks ago by b.d237 • 40
0
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2
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617
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2
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Error : Duplicate allele added to VariantContext GATK
vcf gatk malformed variantstotable written 10 months ago by steven.blanchard92 • 0 • updated 12 weeks ago by brett • 0
0
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0
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140
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0
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Qs about mutect2
gatk wes mutect2 written 12 weeks ago by walker • 10
0
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0
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226
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0
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How can I fix picard error: Sequences at index 0 don't match
gatk picard written 12 weeks ago by Niek De Klein • 2.4k
2
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1
answer
194
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1
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GATK BaseRecalibrator No overlapping contigs found ERROR
reads gatk contigs baserecalibrator written 3 months ago by marongiu.luigi • 350 • updated 3 months ago by Pierre Lindenbaum ♦ 116k
1
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1
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158
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1
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DP and DP at site do not match using only 1 sample in VCF
vcf variant calling gatk written 3 months ago by ajuiwl • 30
1
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0
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212
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0
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Question about Base calling for pacbio data
genome indel pacbio snp gatk written 3 months ago by kamel • 0 • updated 3 months ago by Vijay Lakhujani ♦ 3.5k
0
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0
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229
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0
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Filtering results difference amongst VCF files
gatk snp filtering variants written 3 months ago by prasundutta87 • 290
1
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0
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388
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0
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IncompatibleClassChangeError when running gatk BaseRecalibrator
gatk java baserecalibrator written 3 months ago by marongiu.luigi • 350
1
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0
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450
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0
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Adding read group to bam files from multiplexed samples
gatk picard bam written 5 months ago by serpalma.v • 20 • updated 3 months ago by Biostar ♦♦ 20
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