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2
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Answer: A: RTG vcfeval: number of variants reported by vcfeval is not equal to actual numbe
4.3 years ago by Len Trigg ★ 1.6k
1
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0
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2.6k
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Answer: A: VCF evaluation using RTG.jar vcfeval
4.3 years ago by Len Trigg ★ 1.6k
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0
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1.4k
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Comment: C: Correct reference for Platinum Genomes?
4.7 years ago by Len Trigg ★ 1.6k
2
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1
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1.3k
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Answer: A: Can a command in RTG (or elsewhere) annotate the TP/TN/FP/FN's produced from RTG
4.8 years ago by Len Trigg ★ 1.6k
0
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1
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4.6k
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Comment: C: Why do people not call normal and tumor variant separately for somatic mutation
updated 4.9 years ago by 44k • written 8.8 years ago by ★ 1.6k
0
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0
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Answer: A: PED file format for use with GATK PhaseByTransmission
updated 4.9 years ago by 44k • written 8.9 years ago by ★ 1.6k
4
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1
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5.3k
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Answer: A: Variant calling for MNP
updated 5.0 years ago by 44k • written 9.3 years ago by ★ 1.6k
1
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0
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4.5k
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Comment: C: VCF Record Question
updated 5.0 years ago by 44k • written 9.3 years ago by ★ 1.6k
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0
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3.3k
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Comment: C: How to discover new mutations in a derived strain relative to a reference genome
updated 5.0 years ago by 44k • written 9.3 years ago by ★ 1.6k
0
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1
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3.3k
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Answer: A: How to discover new mutations in a derived strain relative to a reference genome
updated 5.0 years ago by 44k • written 9.3 years ago by ★ 1.6k
8
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1
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8.6k
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Answer: Answer: Should you decompose and normalize multi-allelic variants for comparison / ID as
updated 2.0 years ago by 44k • written 9.3 years ago by ★ 1.6k
2
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1
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7.5k
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Answer: A: Modifying fasta file based on vcf information
updated 5.1 years ago by 44k • written 9.4 years ago by ★ 1.6k
0
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0
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2.3k
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Comment: C: SNP discovery at ambiguous positions - how to keep them and get relevant result
updated 5.2 years ago by 44k • written 9.4 years ago by ★ 1.6k
4
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1
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3.3k
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Comment: C: VCF - what are overlapping variants?
5.4 years ago by Len Trigg ★ 1.6k
1
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0
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2.4k
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Comment: C: why is variant calling difficult?
5.7 years ago by Len Trigg ★ 1.6k
0
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0
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2.7k
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Answer: A: Create a pseudo-haploid fasta file based genotype calls for an individual (vcf f
6.0 years ago by Len Trigg ★ 1.6k
0
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0
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26k
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Comment: C: intersect VCF files
updated 6.2 years ago by 44k • written 7.0 years ago by ★ 1.6k
10
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3
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26k
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Answer: A: intersect VCF files
updated 6.2 years ago by 44k • written 8.7 years ago by ★ 1.6k
0
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1
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1.2k
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Answer: A: Simulating Trio Data
6.3 years ago by Len Trigg ★ 1.6k
1
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1
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4.4k
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Answer: A: Identifying De Novo Mutations from vcf files
6.3 years ago by Len Trigg ★ 1.6k
0
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0
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2.6k
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Comment: C: Constructing a mean ROC curve based on 5 iterations
6.4 years ago by Len Trigg ★ 1.6k
1
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0
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8.2k
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Comment: C: compare SV results across samples - Manta, Delly
6.5 years ago by Len Trigg ★ 1.6k
0
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0
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8.2k
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Comment: C: compare SV results across samples - Manta, Delly
6.5 years ago by Len Trigg ★ 1.6k
3
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1
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8.2k
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Answer: A: compare SV results across samples - Manta, Delly
6.5 years ago by Len Trigg ★ 1.6k
0
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0
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14k
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Comment: C: MAF vs VAF
6.7 years ago by Len Trigg ★ 1.6k
1
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1
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4.3k
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Comment: C: Can you assume variants not in VCF are all monomorphic for the reference allele?
6.7 years ago by Len Trigg ★ 1.6k
1
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0
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3.5k
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Answer: A: Indel concordance from different VCF files
6.8 years ago by Len Trigg ★ 1.6k
1
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1
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1.7k
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Answer: C: SMaSH installation error
6.8 years ago by Len Trigg ★ 1.6k
1
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0
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2.4k
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Comment: C: Strategies to call variants from a cancer sample
7.0 years ago by Len Trigg ★ 1.6k
1
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1
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8.7k
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Comment: C: Edditing headers from a .vcf.gz file
7.0 years ago by Len Trigg ★ 1.6k
0
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2
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1.6k
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Comment: C: Fasted method to genotype given SNPs from NGS data
7.0 years ago by Len Trigg ★ 1.6k
0
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0
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3.8k
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Comment: C: phasing variants to find de novos
7.0 years ago by Len Trigg ★ 1.6k
4
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1
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3.8k
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Comment: C: phasing variants to find de novos
7.1 years ago by Len Trigg ★ 1.6k
0
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0
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3.8k
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Comment: C: phasing variants to find de novos
7.1 years ago by Len Trigg ★ 1.6k
5
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1
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3.8k
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Answer: A: phasing variants to find de novos
7.1 years ago by Len Trigg ★ 1.6k
1
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1
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2.8k
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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
7.2 years ago by Len Trigg ★ 1.6k
3
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0
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4.7k
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Answer: A: How to measure NGS depth coverage bias
7.2 years ago by Len Trigg ★ 1.6k
1
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1
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7.3k
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Answer: A: weird insert size post trimming
7.3 years ago by Len Trigg ★ 1.6k
1
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0
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4.3k
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Comment: C: Correct way of merging samples for father, mother, child trio variant calling
7.4 years ago by Len Trigg ★ 1.6k
6
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0
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3.7k
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Answer: A: Difference between NIST VCF and Illumina Platinum Genomes VCF for NA12878
7.4 years ago by Len Trigg ★ 1.6k
6
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1
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3.3k
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Answer: A: Comparing two VCFs and drawing a precision-recall curve
7.4 years ago by Len Trigg ★ 1.6k
2
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0
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5.9k
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Answer: A: Extract several fields from vcf file
7.5 years ago by Len Trigg ★ 1.6k
3
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1
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3.3k
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Answer: A: Comparing VCF with dbsnp
7.6 years ago by Len Trigg ★ 1.6k
0
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0
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2.6k
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Answer: A: Filtering a Multi-Sample VCF for variants where at least one sample meets the gi
7.6 years ago by Len Trigg ★ 1.6k
1
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0
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8.2k
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Comment: C: VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased
7.7 years ago by Len Trigg ★ 1.6k
0
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1
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15k
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Comment: C: Split a VCF file into individual sample files
7.7 years ago by Len Trigg ★ 1.6k
2
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0
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7.7k
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Answer: A: Remove Single Info Field From Vcf
7.7 years ago by Len Trigg ★ 1.6k
3
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0
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6.4k
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Answer: A: How to add trio information to VCF or PED format (to compute Mendel error in Pli
7.7 years ago by Len Trigg ★ 1.6k
1
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1
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4.0k
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Answer: A: Number of homozygous and heterozygous variants
7.8 years ago by Len Trigg ★ 1.6k
1
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0
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6.9k
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Answer: A: How to "haploidize" diploid SNPs data in a vcf file
7.8 years ago by Len Trigg ★ 1.6k
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