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questions
1
vote
2
replies
322
views
install of genomestudio 2.0.5 in aws
illumina
3 months ago by
bioguy24
▴ 230
0
votes
4
replies
815
views
csv to custom manifest file
illumina
11 months ago by
bioguy24
▴ 230
1
vote
2
replies
620
views
convert illumina manifest to csv
illumina
updated 12 months ago by
rpolicastro
13k • written 12 months ago by
bioguy24
▴ 230
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 1 day ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
6
votes
15
replies
2.4k
views
processing in strelka2 with multiples bam file in directory
strelka2
updated 2.3 years ago by
aldhairmedico
▴ 70 • written 4.3 years ago by
bioguy24
▴ 230
0
votes
1
reply
2.1k
views
STAR-Fusion error while executing and produces some intermediates files
Star-fusion
updated 3.3 years ago by
Kevin Blighe
87k • written 4.9 years ago by
bioguy24
▴ 230
1
vote
1
reply
1.4k
views
Haplotypecaller indel realignment
haplotypecaller
4.3 years ago by
bioguy24
▴ 230
1
vote
2
replies
892
views
sugesstions to optimize an abra2 command
abra2
4.3 years ago by
bioguy24
▴ 230
0
votes
0
replies
556
views
q30 using multicovergebam greater the target length
multibam coverage
updated 4.3 years ago by
Biostar
20 • written 4.4 years ago by
bioguy24
▴ 230
0
votes
0
replies
759
views
calculate per base depth and q30 reads from bam using a bed
samtools depth and q30
4.4 years ago by
bioguy24
▴ 230
2
votes
2
replies
4.0k
views
bedtools 2.25 vs bedtools2.20 coverageBed output not consistent
ngs
bedtools
updated 19 months ago by
Ram
43k • written 8.6 years ago by
bioguy24
▴ 230
1
vote
2
replies
767
views
prepare file for depth of coverage
depth of coverage
4.7 years ago by
bioguy24
▴ 230
0
votes
2
replies
2.0k
views
targets in a bed at or above a coverage
bed
bam
updated 13 months ago by
Ram
43k • written 4.8 years ago by
bioguy24
▴ 230
3
votes
2
replies
1.1k
views
report every base in a bam using bed as input
samtools
bcftools
updated 4.9 years ago by
Pierre Lindenbaum
161k • written 4.9 years ago by
bioguy24
▴ 230
0
votes
1
reply
1.9k
views
correct mark duplicated error using python and pysam to filter out secondary alignments
python
pysam
5.0 years ago by
bioguy24
▴ 230
3
votes
4
replies
2.4k
views
error using bqsr and incompatible contigs
gatk
bqsr
updated 5.3 years ago by
Biostar
20 • written 5.7 years ago by
bioguy24
▴ 230
4
votes
5
replies
5.4k
views
samtools covert to bam, sort and index all gz.sam
samtools
parellel
updated 5.3 years ago by
cmdcolin
★ 3.8k • written 5.3 years ago by
bioguy24
▴ 230
1
vote
2
replies
2.9k
views
using vcftools to add gene name to vcf file
vcftools
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
bioguy24
▴ 230
1
vote
2
replies
2.9k
views
add gene name from bed file to vcf in vcftools
vcftools
updated 21 months ago by
Ram
43k • written 8.2 years ago by
bioguy24
▴ 230
2
votes
2
replies
2.3k
views
gatk vqsr --recal-file error
gatk
vqsr
updated 5.7 years ago by
Santosh Anand
5.7k • written 5.7 years ago by
bioguy24
▴ 230
2
votes
5
replies
3.7k
views
GATK MarkDuplicates output and bam
GATK
MarkDuplicates
updated 5.7 years ago by
finswimmer
16k • written 5.7 years ago by
bioguy24
▴ 230
3
votes
4
replies
2.8k
views
multithread support for gatk
gatk
bqsr
5.7 years ago by
bioguy24
▴ 230
6
votes
6
replies
4.0k
views
using bash variable in picard MarkDuplicates command
ngs
picard
updated 5.7 years ago by
h.mon
35k • written 5.7 years ago by
bioguy24
▴ 230
1
vote
3
replies
1.5k
views
illumina data analysis with bwa mem
bwa mem
updated 5.8 years ago by
Devon Ryan
104k • written 5.8 years ago by
bioguy24
▴ 230
5
votes
2
replies
2.6k
views
bcftools split and filter variants in vcf
ngs
bcftools
updated 6.2 years ago by
Kevin Blighe
87k • written 6.2 years ago by
bioguy24
▴ 230
1
vote
3
replies
5.4k
views
bedtools coverage bed
NGS
bedtools
updated 6.3 years ago by
Alex Reynolds
35k • written 6.3 years ago by
bioguy24
▴ 230
2
votes
6
replies
1.4k
views
NGS variant prioritization tools/script
NGS
updated 6.3 years ago by
GenoMax
141k • written 6.3 years ago by
bioguy24
▴ 230
2
votes
6
replies
2.2k
views
add coordinates to line of output extracted from vcf
genotype
vcf
6.4 years ago by
bioguy24
▴ 230
0
votes
1
reply
1.2k
views
integrate pharmGKB data with annovar
ngs
updated 6.6 years ago by
Kevin Blighe
87k • written 6.6 years ago by
bioguy24
▴ 230
4
votes
3
replies
6.0k
views
calculate average target coverage from bam file
ngs
updated 6.6 years ago by
DG
7.3k • written 6.6 years ago by
bioguy24
▴ 230
0
votes
1
reply
2.3k
views
IGV pileup not showing any reads at any position in bam
NGS
6.8 years ago by
bioguy24
▴ 230
3
votes
4
replies
1.4k
views
search a large dbsnp file using another most efficiently
ngs
6.8 years ago by
bioguy24
▴ 230
3
votes
2
replies
3.1k
views
adding custom INFO tag to vcf
NGS
vcf
updated 6.9 years ago by
Pierre Lindenbaum
161k • written 6.9 years ago by
bioguy24
▴ 230
6
votes
5
replies
1.6k
views
hg19 transcript mapping or exon overlap
NGS
updated 6.9 years ago by
pjalali46
▴ 10 • written 6.9 years ago by
bioguy24
▴ 230
2
votes
4
replies
1.3k
views
bash repeat file names if in directory after executing NGS tools
NGS
7.0 years ago by
bioguy24
▴ 230
1
vote
1
reply
911
views
associate a variant with a mutation in hg19
ngs
updated 7.1 years ago by
Petr Ponomarenko
★ 2.8k • written 7.1 years ago by
bioguy24
▴ 230
3
votes
3
replies
1.9k
views
add undefined annotations from vcf files
bcftools
7.1 years ago by
bioguy24
▴ 230
0
votes
1
reply
1.7k
views
Bash to match and store numerical prefix to update files
ngs
bash
7.2 years ago by
bioguy24
▴ 230
6
votes
6
replies
4.9k
views
Calculate forward and reverse strand reads from bam
ngs
updated 7.2 years ago by
michael.ante
★ 3.8k • written 7.2 years ago by
bioguy24
▴ 230
5
votes
8
replies
2.7k
views
lift coordinates mapping to_alt chromosomes in hg38
ngs
bed
updated 13 months ago by
Ram
43k • written 7.3 years ago by
bioguy24
▴ 230
3
votes
7
replies
4.5k
views
convert hg38 variant calls to hg19
ngs
updated 7.3 years ago by
Pierre Lindenbaum
161k • written 7.3 years ago by
bioguy24
▴ 230
8
votes
4
replies
5.0k
views
genes that map to hg38 coordinates
ngs
7.3 years ago by
bioguy24
▴ 230
1
vote
5
replies
1.7k
views
current transcipt given genelist
ngs
7.3 years ago by
bioguy24
▴ 230
9
votes
4
replies
3.0k
views
Batch download of hg19 sequences in bed file
ngs
FASTA
Bed
updated 7.3 years ago by
genecats.ucsc
▴ 580 • written 7.3 years ago by
bioguy24
▴ 230
0
votes
0
replies
1.5k
views
correct variant position in vcf following HGVS guidelines
ngs
vcf
7.4 years ago by
bioguy24
▴ 230
1
vote
2
replies
8.5k
views
vcf compare between 2 vcf files using vcf tools
vcftools
updated 13 months ago by
Ram
43k • written 7.4 years ago by
bioguy24
▴ 230
5
votes
8
replies
2.6k
views
update unknown enteries in bed with gene names
ngs
updated 7.4 years ago by
Alex Reynolds
35k • written 7.4 years ago by
bioguy24
▴ 230
1
vote
3
replies
1.4k
views
list variants that map to a genomic location
ngs
7.7 years ago by
bioguy24
▴ 230
1
vote
2
replies
1.6k
views
current version of transcript using NCBI ID
ngs
7.7 years ago by
bioguy24
▴ 230
0
votes
2
replies
1.6k
views
current version of transcript using mysql
mysql
7.7 years ago by
bioguy24
▴ 230
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