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1
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3
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1.3k
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Fastest way to switch out sites on one BCF for sites in another BCF?
bcftools bcf vcf
5.4 years ago by curious ▴ 900
0
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0
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8.2k
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Comment: C: sorting a multi-sample (genotype) vcf file
5.4 years ago by curious ▴ 900
0
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0
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3.3k
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Comment: C: Speed of merging multiple bcfs with bcftools compared to PLINK?
5.4 years ago by curious ▴ 900
5
votes
2
replies
3.3k
views
Speed of merging multiple bcfs with bcftools compared to PLINK?
bcftools plink
5.4 years ago by curious ▴ 900
1
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0
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2.4k
views
Comment: C: Doing an operation on one huge VCF, use Python or would C be faster (somewhat ni
5.4 years ago by curious ▴ 900
0
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0
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7.1k
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Comment: C: Flipping every REF/ALT and corresponsing genotypes of every single indel in a VC
5.4 years ago by curious ▴ 900
0
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1
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7.1k
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Comment: C: Flipping every REF/ALT and corresponsing genotypes of every single indel in a VC
5.4 years ago by curious ▴ 900
3
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4
replies
7.1k
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Flipping every REF/ALT and corresponsing genotypes of every single indel in a VCF.
bcftools oxford plink
5.4 years ago by curious ▴ 900
0
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0
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8.7k
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Comment: C: Cannot install snpStats packages
5.4 years ago by curious ▴ 900
0
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1
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1.3k
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Comment: C: Using bcftools merge on the output of multiple process substitution? (somewhat a
5.4 years ago by curious ▴ 900
2
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3
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1.3k
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Using bcftools merge on the output of multiple process substitution? (somewhat a linux question)
linux
5.4 years ago by curious ▴ 900
0
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1
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2.4k
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Comment: C: Doing an operation on one huge VCF, use Python or would C be faster (somewhat ni
5.5 years ago by curious ▴ 900
1
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4
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2.4k
views
Doing an operation on one huge VCF, use Python or would C be faster (somewhat niave bcftools/computer science question)
python bcftools c vcf
5.5 years ago by curious ▴ 900
2
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1
reply
2.8k
views
Comment: C: What is the current standard for HLA allele typing prediction from SNP data?
5.5 years ago by curious ▴ 900
1
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0
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3.1k
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Comment: C: Michigan imputation server quality control failed
5.5 years ago by curious ▴ 900
0
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0
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894
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Removing rare variants from SNP array before imputation then putting them back in after imputation?
imputation snp array
5.5 years ago by curious ▴ 900
0
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0
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3.2k
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Comment: C: Michigan Imputation Server - typed-only sites?
5.5 years ago by curious ▴ 900
4
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0
replies
4.3k
views
Answer: A: How to force GATK haplotypecaller to output all genomic position (even non varia
5.5 years ago by curious ▴ 900
0
votes
0
replies
836
views
what does: "Allele mismatch Ref:G/T" mean in the QC report from the michigan imputation server?
imputation
5.5 years ago by curious ▴ 900
0
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0
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1.1k
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Trying to figure out coordinates for long range LD regions on build 38 for flashpca
flashpca ld
5.5 years ago by curious ▴ 900
0
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0
replies
1.0k
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Comment: C: simple question about insertion standards in vcf 4.2
5.6 years ago by curious ▴ 900
1
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3
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1.0k
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simple question about insertion standards in vcf 4.2
vcf specificaiton
updated 5.6 years ago by 11k • written 5.6 years ago by ▴ 900
0
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0
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889
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**Is nonreference discordance just (Number of ALT mismatches/Number of ALT matches)*100?**
vcf-compare vcf
5.6 years ago by curious ▴ 900
0
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0
replies
7.1k
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Comment: C: VCF to BCF conversion with bcftools?
5.6 years ago by curious ▴ 900
0
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0
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7.1k
views
Comment: C: VCF to BCF conversion with bcftools?
5.6 years ago by curious ▴ 900
5
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4
replies
7.1k
views
VCF to BCF conversion with bcftools?
bcftools
updated 5.6 years ago by 166k • written 5.6 years ago by ▴ 900
2
votes
2
replies
13k
views
Comment: C: bcftools selest sites with FILTER "PASS" or "."
5.7 years ago by curious ▴ 900
18
votes
5
replies
13k
views
bcftools selest sites with FILTER "PASS" or "."
bcftools
updated 5.7 years ago by 166k • written 5.7 years ago by ▴ 900
1
vote
3
replies
901
views
Standard approach for telling if sites were removed during calling due to poor quality or non-variant?
gatk vcf
5.7 years ago by curious ▴ 900
0
votes
1
reply
901
views
Comment: C: Standard approach for telling if variants were removed during calling due to poo
5.7 years ago by curious ▴ 900
1
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0
replies
1.8k
views
Comment: C: python type error
5.7 years ago by curious ▴ 900
0
votes
0
replies
849
views
Standard cutoffs for call-rate when filtering a VCF?
gatk vcf
5.7 years ago by curious ▴ 900
0
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0
replies
5.1k
views
Comment: C: How can I create an Illumina report in Linux using IDAT files?
5.7 years ago by curious ▴ 900
1
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1
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5.1k
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Answer: C: How can I create an Illumina report in Linux using IDAT files?
5.7 years ago by curious ▴ 900
0
votes
0
replies
10k
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Comment: C: How to Collapse Bedtools reciprocal overlap regions
5.7 years ago by curious ▴ 900
1
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0
replies
101k
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Comment: C: Extract Sub-Set Of Regions From Vcf File
5.7 years ago by curious ▴ 900
0
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0
replies
5.9k
views
Comment: C: conda/bioconda installation of plink fails
5.7 years ago by curious ▴ 900
2
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1
reply
5.9k
views
Answer: A: conda/bioconda installation of plink fails
5.7 years ago by curious ▴ 900
0
votes
0
replies
4.5k
views
Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
5.7 years ago by curious ▴ 900
0
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1
reply
4.5k
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
5.7 years ago by curious ▴ 900
0
votes
1
reply
11k
views
Comment: C: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With G
5.7 years ago by curious ▴ 900
5
votes
8
replies
4.5k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk variant calling sureselect
updated 17 months ago by 45k • written 5.7 years ago by ▴ 900
0
votes
0
replies
1.0k
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Is it a convention for displaying human males in VCF as homozygous diploid?
vcf diploid
5.7 years ago by curious ▴ 900
0
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1
reply
2.2k
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Comment: C: Creating a GenomicsDBImport from the normal Mutect2 calls
5.7 years ago by curious ▴ 900
0
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0
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1.5k
views
Comment: C: Good quality control metrics to look out for when someone gives you BAMs
5.7 years ago by curious ▴ 900
0
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0
replies
1.5k
views
Comment: C: how to find haplotype of SNPs
5.7 years ago by curious ▴ 900
0
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1
reply
1.5k
views
Comment: C: how to find haplotype of SNPs
5.7 years ago by curious ▴ 900
0
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1
reply
2.2k
views
Comment: C: Creating a GenomicsDBImport from the normal Mutect2 calls
5.7 years ago by curious ▴ 900
1
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0
replies
4.6k
views
Comment: C: What are some references of works that use a TPM expression threshold for filter
5.7 years ago by curious ▴ 900
0
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1
reply
1.5k
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Comment: C: Good quality control metrics to look out for when someone gives you BAMs
5.7 years ago by curious ▴ 900
316 results • Page 5 of 7
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