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1
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638
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Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
gatk
updated 5 days ago by 90k • written 5 weeks ago by ▴ 900
0
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0
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6.6k
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Comment: Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
6 weeks ago by curious ▴ 900
2
votes
2
replies
2.5k
views
Help understanding this per base sequence content failure fastqc plot
fastqc
updated 6 weeks ago by 16k • written 7 weeks ago by ▴ 900
0
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1
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6.6k
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Comment: Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
7 weeks ago by curious ▴ 900
4
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5
replies
6.6k
views
Does this adapter content from fastqc to warrant trimming prior to alignment?
fastqc bwa-mem multiqc
6 weeks ago by curious ▴ 900
0
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0
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1.4k
views
Comment: Comment: ERROR::INVALID_TAG_NM:Record A, Read name B, NM tag (nucleotide differences) in
5 months ago by curious ▴ 900
0
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2
replies
1.4k
views
ERROR::INVALID_TAG_NM:Record A, Read name B, NM tag (nucleotide differences) in file [0] does not match reality [1]
bwa
5 months ago by curious ▴ 900
0
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1
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1.1k
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Comment: Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
5 months ago by curious ▴ 900
0
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0
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1.1k
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Comment: Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
5 months ago by curious ▴ 900
0
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4
replies
1.1k
views
Why am I getting the exact same MarkDuplicates results when passing a query or coordinate sorted bam?
picard bwa
updated 5 months ago by 154k • written 5 months ago by ▴ 900
0
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1
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1.4k
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Comment: Comment: How to preserve full FASTQ header through alignment and CRAM recovery
5 months ago by curious ▴ 900
4
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5
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1.4k
views
How to preserve full FASTQ header through alignment and CRAM recovery
bam fastq cram
updated 5 months ago by 154k • written 5 months ago by ▴ 900
0
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1
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2.1k
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Comment: Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
6 months ago by curious ▴ 900
0
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0
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2.1k
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Comment: Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
6 months ago by curious ▴ 900
9
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11
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2.1k
views
How common is it to split fastq files prior to bwa mem to increase parallelization?
mem bwa alignment
updated 5 months ago by 4.7k • written 6 months ago by ▴ 900
2
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1
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2.1k
views
Comment: Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
6 months ago by curious ▴ 900
0
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2
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1.1k
views
What do the transcript variant # mean in RefSeq?
refseq
updated 18 months ago by 45k • written 18 months ago by ▴ 900
0
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0
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769
views
Comment: Comment: How to convert Haps file to vcf file?
18 months ago by curious ▴ 900
0
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5
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2.2k
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 18 months ago by 11k • written 18 months ago by ▴ 900
0
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0
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2.2k
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Comment: Comment: Easy way to find out which allele is minor allele from bed file?
18 months ago by curious ▴ 900
0
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1
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2.2k
views
Comment: Comment: Easy way to find out which allele is minor allele from bed file?
18 months ago by curious ▴ 900
0
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0
replies
881
views
Comment: Comment: Can't figure out plink --sample-diff
19 months ago by curious ▴ 900
0
votes
2
replies
881
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Can't figure out plink --sample-diff
plink
19 months ago by curious ▴ 900
0
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0
replies
1.1k
views
Comment: Comment: Why do these two variants appear to result in the same amino acid change when an
21 months ago by curious ▴ 900
3
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2
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1.1k
views
Why do these two variants appear to result in the same amino acid change when annotated by snpeff, but are annotated differently in clinvar
clinvar
21 months ago by curious ▴ 900
1
vote
1
reply
847
views
Is there a way to map Medgen # to OMIM # programmatically?
medgen omim
updated 22 months ago by 166k • written 22 months ago by ▴ 900
0
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1
reply
1.4k
views
Where do these snpeff annotation come from?
snpeff
updated 23 months ago by 103k • written 23 months ago by ▴ 900
0
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4
replies
2.2k
views
Is there a way to get a list of all homogygous sites for each sample with plink (regardless if they are in a run)
plink
updated 2.2 years ago by 11k • written 2.2 years ago by ▴ 900
0
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1
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2.2k
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Comment: Comment: Is there a way to get a list of all homogygous sites for each sample with plink
2.2 years ago by curious ▴ 900
1
vote
1
reply
880
views
bcftools update ID keeping only string after ';'
bcftools
updated 2.2 years ago by 166k • written 2.2 years ago by ▴ 900
0
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1
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1.5k
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Comment: Comment: Is this a valid allele in a vcf?
2.3 years ago by curious ▴ 900
0
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1
reply
1.5k
views
Comment: Comment: Is this a valid allele in a vcf?
2.3 years ago by curious ▴ 900
0
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5
replies
1.5k
views
Is this a valid allele in a vcf?
vcf
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 900
0
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1
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1.5k
views
Comment: Comment: Is it possible to interpret HGVS without transcript version number?
2.3 years ago by curious ▴ 900
0
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1
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1.5k
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Comment: Comment: Is it possible to interpret HGVS without transcript version number?
2.3 years ago by curious ▴ 900
0
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0
replies
880
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Comment: Comment: jannovar download problem
2.3 years ago by curious ▴ 900
0
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6
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1.5k
views
Is it possible to interpret HGVS without transcript version number?
hgvs
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by ▴ 900
0
votes
2
replies
880
views
jannovar download problem
jannovar
2.3 years ago by curious ▴ 900
0
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0
replies
1.2k
views
Comment: Comment: Why does this stop gained result in a longer protein than the canonical version
2.4 years ago by curious ▴ 900
2
votes
2
replies
1.2k
views
Why does this stop gained result in a longer protein than the canonical version
ensembl
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 900
2
votes
2
replies
3.7k
views
Download VCF for dbsnp 156?
dbsnp
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 900
0
votes
1
reply
833
views
Any way to get bcftools to query up to but not including the last site given in a region query
bcftools
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 900
4
votes
3
replies
2.6k
views
What does canonical transcript mean in the context of VEP
vep
updated 2.5 years ago by 4.8k • written 2.5 years ago by ▴ 900
0
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0
replies
981
views
Comment: Comment: How to check the imputation quality of genotyping files?
2.5 years ago by curious ▴ 900
0
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0
replies
1.8k
views
Comment: Comment: Low SNP Overlap with Michigan 1KG and TopMed reference panel
2.5 years ago by curious ▴ 900
0
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0
replies
1.6k
views
Comment: Comment: viewing hgvs in genome data viewer
2.5 years ago by curious ▴ 900
0
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1
reply
1.6k
views
Comment: Comment: viewing hgvs in genome data viewer
2.5 years ago by curious ▴ 900
1
vote
4
replies
1.6k
views
viewing hgvs in genome data viewer
ncbi hgvs clinvar
2.5 years ago by curious ▴ 900
0
votes
0
replies
696
views
Trying to understand the difference between between these two HGVS
hgvs
2.8 years ago by curious ▴ 900
2
votes
2
replies
1.4k
views
drop duplicate insertion deletions in VCF at same position while keeping one
bcftools
2.8 years ago by curious ▴ 900
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