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Comment: C: Michigan Imputation Server - typed-only sites?
4.6 years ago by curious ▴ 820
4
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3.7k
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Answer: A: How to force GATK haplotypecaller to output all genomic position (even non varia
4.6 years ago by curious ▴ 820
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728
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what does: "Allele mismatch Ref:G/T" mean in the QC report from the michigan imputation server?
imputation
4.6 years ago by curious ▴ 820
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0
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833
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Trying to figure out coordinates for long range LD regions on build 38 for flashpca
flashpca ld
4.7 years ago by curious ▴ 820
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0
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742
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Comment: C: simple question about insertion standards in vcf 4.2
4.7 years ago by curious ▴ 820
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3
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742
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simple question about insertion standards in vcf 4.2
vcf specificaiton
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 820
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0
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762
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**Is nonreference discordance just (Number of ALT mismatches/Number of ALT matches)*100?**
vcf-compare vcf
4.7 years ago by curious ▴ 820
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0
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6.3k
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Comment: C: VCF to BCF conversion with bcftools?
4.8 years ago by curious ▴ 820
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0
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6.3k
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Comment: C: VCF to BCF conversion with bcftools?
4.8 years ago by curious ▴ 820
5
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4
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6.3k
views
VCF to BCF conversion with bcftools?
bcftools
updated 4.8 years ago by 164k • written 4.8 years ago by ▴ 820
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2
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11k
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Comment: C: bcftools selest sites with FILTER "PASS" or "."
4.8 years ago by curious ▴ 820
14
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5
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11k
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bcftools selest sites with FILTER "PASS" or "."
bcftools
updated 4.8 years ago by 164k • written 4.8 years ago by ▴ 820
1
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3
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683
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Standard approach for telling if sites were removed during calling due to poor quality or non-variant?
gatk vcf
4.8 years ago by curious ▴ 820
0
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1
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683
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Comment: C: Standard approach for telling if variants were removed during calling due to poo
4.8 years ago by curious ▴ 820
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0
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1.4k
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Comment: C: python type error
4.8 years ago by curious ▴ 820
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0
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738
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Standard cutoffs for call-rate when filtering a VCF?
gatk vcf
4.8 years ago by curious ▴ 820
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0
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4.0k
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Comment: C: How can I create an Illumina report in Linux using IDAT files?
4.8 years ago by curious ▴ 820
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1
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4.0k
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Answer: C: How can I create an Illumina report in Linux using IDAT files?
4.8 years ago by curious ▴ 820
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0
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8.4k
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Comment: C: How to Collapse Bedtools reciprocal overlap regions
4.8 years ago by curious ▴ 820
1
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0
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94k
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Comment: C: Extract Sub-Set Of Regions From Vcf File
4.8 years ago by curious ▴ 820
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0
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4.5k
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Comment: C: conda/bioconda installation of plink fails
4.8 years ago by curious ▴ 820
2
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1
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4.5k
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Answer: A: conda/bioconda installation of plink fails
4.8 years ago by curious ▴ 820
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0
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3.7k
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
4.8 years ago by curious ▴ 820
0
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1
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3.7k
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Comment: C: Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
4.8 years ago by curious ▴ 820
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1
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11k
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Comment: C: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With G
4.8 years ago by curious ▴ 820
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8
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3.7k
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Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk variant calling sureselect
updated 6 months ago by 44k • written 4.8 years ago by ▴ 820
0
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0
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856
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Is it a convention for displaying human males in VCF as homozygous diploid?
vcf diploid
4.8 years ago by curious ▴ 820
0
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1
reply
1.6k
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Comment: C: Creating a GenomicsDBImport from the normal Mutect2 calls
4.8 years ago by curious ▴ 820
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0
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1.2k
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Comment: C: Good quality control metrics to look out for when someone gives you BAMs
4.8 years ago by curious ▴ 820
0
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0
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1.1k
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Comment: C: how to find haplotype of SNPs
4.9 years ago by curious ▴ 820
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1
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1.1k
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Comment: C: how to find haplotype of SNPs
4.9 years ago by curious ▴ 820
0
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1
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1.6k
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Comment: C: Creating a GenomicsDBImport from the normal Mutect2 calls
4.9 years ago by curious ▴ 820
1
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0
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3.3k
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Comment: C: What are some references of works that use a TPM expression threshold for filter
4.9 years ago by curious ▴ 820
0
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1
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1.2k
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Comment: C: Good quality control metrics to look out for when someone gives you BAMs
4.9 years ago by curious ▴ 820
0
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4
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1.2k
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Good quality control metrics to look out for when someone gives you BAMs
bam qc
4.9 years ago by curious ▴ 820
0
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0
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2.7k
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Comment: C: filter VCF based on info field that has a key but no value
4.9 years ago by curious ▴ 820
0
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0
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2.7k
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Comment: C: filter VCF based on info field that has a key but no value
4.9 years ago by curious ▴ 820
1
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0
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1.3k
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Comment: C: Genetic map for chromosome X that shows recombination rates?
4.9 years ago by curious ▴ 820
1
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2
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1.3k
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Genetic map for chromosome X that shows recombination rates?
shapeit phasing
updated 4.9 years ago by 88k • written 4.9 years ago by ▴ 820
0
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0
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4.6k
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Comment: C: update-chr issues with PLINK 1.9
4.9 years ago by curious ▴ 820
0
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1
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4.6k
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Comment: C: update-chr issues with PLINK 1.9
4.9 years ago by curious ▴ 820
1
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0
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2.6k
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Comment: A: Laptop specs for Bioinformatic analyses
4.9 years ago by curious ▴ 820
0
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0
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958
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Trouble understanding Eagle2 phasing software "--allowRefAltSwap" flag
eagle phasing
4.9 years ago by curious ▴ 820
0
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0
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1.1k
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Comment: C: A2 different between PLINK .bim file and .frq file?
4.9 years ago by curious ▴ 820
0
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0
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1.7k
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Comment: C: ImportError: No module named cutadapt.scripts
4.9 years ago by curious ▴ 820
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2
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1.1k
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A2 different between PLINK .bim file and .frq file?
plink
updated 4.9 years ago by 11k • written 4.9 years ago by ▴ 820
0
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0
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1.4k
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Evaluating switch error rate when phasing with Eagle2?
phasing gwas eagle beagle
4.9 years ago by curious ▴ 820
0
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0
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1.2k
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When using Eagle, is the X chromosome typically phased without including pseudoautosomal regions?
eagle phasing
4.9 years ago by curious ▴ 820
0
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0
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2.4k
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Comment: C: Is there a way to force a specific order for variants in a PLINK file that have
5.0 years ago by curious ▴ 820
0
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1
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2.4k
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Comment: C: Is there a way to force a specific order for variants in a PLINK file that have
5.0 years ago by curious ▴ 820
300 results • Page 5 of 6
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