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Answer: A: RTG vcfeval: number of variants reported by vcfeval is not equal to actual numbe
3.7 years ago by Len Trigg ★ 1.6k
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Answer: A: VCF evaluation using RTG.jar vcfeval
3.7 years ago by Len Trigg ★ 1.6k
2
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1
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1.2k
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Answer: A: Can a command in RTG (or elsewhere) annotate the TP/TN/FP/FN's produced from RTG
4.2 years ago by Len Trigg ★ 1.6k
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0
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Answer: A: PED file format for use with GATK PhaseByTransmission
updated 4.3 years ago by 43k • written 8.3 years ago by ★ 1.6k
4
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Answer: A: Variant calling for MNP
updated 4.4 years ago by 43k • written 8.7 years ago by ★ 1.6k
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Answer: A: How to discover new mutations in a derived strain relative to a reference genome
updated 4.4 years ago by 43k • written 8.7 years ago by ★ 1.6k
8
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Answer: Answer: Should you decompose and normalize multi-allelic variants for comparison / ID as
updated 17 months ago by 43k • written 8.8 years ago by ★ 1.6k
2
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7.0k
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Answer: A: Modifying fasta file based on vcf information
updated 4.5 years ago by 43k • written 8.8 years ago by ★ 1.6k
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Answer: A: Create a pseudo-haploid fasta file based genotype calls for an individual (vcf f
5.4 years ago by Len Trigg ★ 1.6k
10
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3
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24k
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Answer: A: intersect VCF files
updated 5.6 years ago by 43k • written 8.2 years ago by ★ 1.6k
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1.2k
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Answer: A: Simulating Trio Data
5.7 years ago by Len Trigg ★ 1.6k
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4.0k
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Answer: A: Identifying De Novo Mutations from vcf files
5.7 years ago by Len Trigg ★ 1.6k
3
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7.5k
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Answer: A: compare SV results across samples - Manta, Delly
5.9 years ago by Len Trigg ★ 1.6k
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0
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3.2k
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Answer: A: Indel concordance from different VCF files
6.2 years ago by Len Trigg ★ 1.6k
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1
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1.5k
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Answer: C: SMaSH installation error
6.2 years ago by Len Trigg ★ 1.6k
5
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1
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3.4k
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Answer: A: phasing variants to find de novos
6.5 years ago by Len Trigg ★ 1.6k
3
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0
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4.4k
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Answer: A: How to measure NGS depth coverage bias
6.6 years ago by Len Trigg ★ 1.6k
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1
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6.5k
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Answer: A: weird insert size post trimming
6.7 years ago by Len Trigg ★ 1.6k
6
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0
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3.6k
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Answer: A: Difference between NIST VCF and Illumina Platinum Genomes VCF for NA12878
6.8 years ago by Len Trigg ★ 1.6k
6
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1
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3.1k
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Answer: A: Comparing two VCFs and drawing a precision-recall curve
6.8 years ago by Len Trigg ★ 1.6k
2
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0
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5.6k
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Answer: A: Extract several fields from vcf file
6.9 years ago by Len Trigg ★ 1.6k
3
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1
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3.1k
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Answer: A: Comparing VCF with dbsnp
7.0 years ago by Len Trigg ★ 1.6k
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0
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2.4k
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Answer: A: Filtering a Multi-Sample VCF for variants where at least one sample meets the gi
7.0 years ago by Len Trigg ★ 1.6k
2
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0
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7.5k
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Answer: A: Remove Single Info Field From Vcf
7.1 years ago by Len Trigg ★ 1.6k
3
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0
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6.0k
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Answer: A: How to add trio information to VCF or PED format (to compute Mendel error in Pli
7.1 years ago by Len Trigg ★ 1.6k
1
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1
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3.7k
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Answer: A: Number of homozygous and heterozygous variants
7.2 years ago by Len Trigg ★ 1.6k
1
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0
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6.4k
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Answer: A: How to "haploidize" diploid SNPs data in a vcf file
7.2 years ago by Len Trigg ★ 1.6k
2
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1
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2.2k
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Answer: A: GA4GH hap.py understanding
7.4 years ago by Len Trigg ★ 1.6k
10
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0
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20k
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Answer: A: Best way to compare two samples in a VCF file
7.4 years ago by Len Trigg ★ 1.6k
2
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1
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3.3k
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Answer: A: Non-cancer somatic mutation calling
7.9 years ago by Len Trigg ★ 1.6k
5
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0
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5.2k
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Answer: A: How Does Left-Alignment Work For Indels? Does It Address All Complicated Issues
7.9 years ago by Len Trigg ★ 1.6k
2
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0
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2.9k
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Answer: A: How is QUAL score calculated in multigenome VCF file?
8.0 years ago by Len Trigg ★ 1.6k
2
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0
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5.3k
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Answer: A: MuTect2's variants missing QUAL score
8.1 years ago by Len Trigg ★ 1.6k
1
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0
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4.0k
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Answer: A: mapping metagenomics samples to multiple references genome
8.5 years ago by Len Trigg ★ 1.6k
1
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1
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2.3k
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Answer: Answer: indel position in repetitive regions
updated 19 months ago by 43k • written 8.5 years ago by ★ 1.6k
0
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0
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1.9k
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Answer: Answer: Convert reads alginment results of NGS metagenomic sample into abundance score
updated 18 months ago by 43k • written 8.6 years ago by ★ 1.6k
1
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0
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1.6k
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Answer: Answer: Theoretical genome sequence
updated 18 months ago by 43k • written 8.7 years ago by ★ 1.6k
13
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1
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24k
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Answer: Answer: Variant call format (VCF) file, how to get statistics per sample?
updated 18 months ago by 43k • written 8.7 years ago by ★ 1.6k
0
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0
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4.5k
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Answer: Answer: VCF genotype generator
updated 18 months ago by 43k • written 8.7 years ago by ★ 1.6k
2
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0
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1.6k
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Answer: Answer: Need recommendations for Family aware Variant/indel caller for WGS data
updated 18 months ago by 43k • written 8.7 years ago by ★ 1.6k
1
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0
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8.6k
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Answer: Answer: randomly shuffle BAM file
updated 17 months ago by 43k • written 8.7 years ago by ★ 1.6k
0
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0
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6.9k
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Answer: A: How to align DNA reads against a database of protein references
8.8 years ago by Len Trigg ★ 1.6k
1
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0
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2.5k
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Answer: Answer: Sensitivity of variant calling
updated 16 months ago by 43k • written 8.8 years ago by ★ 1.6k
1
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0
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6.5k
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Answer: Answer: How to handle chr Y data in BAM files from exome sequencing of human females
updated 15 months ago by 43k • written 8.9 years ago by ★ 1.6k
2
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0
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1.9k
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Answer: Answer: GATK creating hs_err_pid.log file
updated 15 months ago by 43k • written 8.9 years ago by ★ 1.6k
1
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0
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5.2k
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Answer: Answer: SNP calling pipeline - testing different programs
updated 14 months ago by 43k • written 8.9 years ago by ★ 1.6k
0
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1
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4.1k
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Answer: Answer: How to identify Denovo Mutations in the child compared with parents?
updated 14 months ago by 43k • written 9.0 years ago by ★ 1.6k
1
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0
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5.6k
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Answer: Answer: What are acceptable SNP QUAL and GQ thresholds to filter on?
updated 14 months ago by 43k • written 9.0 years ago by ★ 1.6k
0
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0
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4.7k
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Answer: Answer: Generate genotype specific FASTA sequences from VCF file and reference sequence
updated 21 months ago by 43k • written 9.0 years ago by ★ 1.6k
2
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0
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4.7k
views
Answer: Answer: Multiple VCF file comparision
updated 21 months ago by 43k • written 9.0 years ago by ★ 1.6k
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