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questions
4
votes
3
replies
2.4k
views
Using ref.fa (with random contig) on bam file aligned without random contigs
VCF
samtools
RNA-Seq
bcftools
updated 2.1 years ago by
Ram
44k • written 8.3 years ago by
umn_bist
▴ 390
7
votes
8
replies
3.9k
views
Reference and dbSNP incompatibility issue (MuTect2)
ucsc.hg19.fa
GATK
RNA-Seq
dbSNP
Mutect2
updated 22 months ago by
Ram
44k • written 8.3 years ago by
umn_bist
▴ 390
2
votes
3
replies
2.9k
views
Request for karyotypically sorted Ensembl reference fasta and its dbSNP vcf for GATK workflow
GATK
RNA-Seq
GrCh37
dbSNP
ensembl
updated 22 months ago by
Ram
44k • written 8.3 years ago by
umn_bist
▴ 390
7
votes
2
replies
7.5k
views
Change chromosome notation to match a new reference
RNA-Seq
updated 8.3 years ago by
Chris Miller
22k • written 8.3 years ago by
umn_bist
▴ 390
5
votes
10
replies
3.7k
views
Automating pre-alignment (and post-alignment) quality control
RNA-Seq
FastQC
Quality Control
updated 8.3 years ago by
harold.smith.tarheel
★ 4.9k • written 8.3 years ago by
umn_bist
▴ 390
8
votes
9
replies
2.8k
views
Mixed opinions on somatic variant calling method
RNA-Seq
somatic mutation
variant caller
8.3 years ago by
umn_bist
▴ 390
7
votes
2
replies
3.8k
views
Calling variants in blood tumor samples without matched normal samples
TCGA
CTC
Unmatched-normal
updated 8.3 years ago by
Chris Miller
22k • written 8.3 years ago by
umn_bist
▴ 390
9
votes
7
replies
8.6k
views
(samtools) Filtering and interpreting >100 QUAL scores
pileup
vcf
phred-scaled-QUAL
samtools
updated 22 months ago by
Ram
44k • written 8.3 years ago by
umn_bist
▴ 390
0
votes
1
reply
4.0k
views
TCGA database search
RNA-Seq
updated 8.4 years ago by
always_learning
★ 1.1k • written 8.4 years ago by
umn_bist
▴ 390
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