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17
votes
5
answers
7.1k
views
10 follow
5
answers
What Is The Fastest Method To Determine The Number Of Positions In A Bam File With >N Coverage?
bedtools depth-of-coverage bam samtools coverage written 5.8 years ago by Malachi Griffith ♦ 17k • updated 3 months ago by Paul • 1.3k
5
votes
3
answers
1.9k
views
3
answers
What Are The Next Steps For Processing Indels From Gatk
indel gatk depth-of-coverage filtering written 5.8 years ago by bari1 • 40 • updated 2.0 years ago by Biostar ♦♦ 20
0
votes
1
answer
1.9k
views
1
answer
Gatk Depthofcoverage Sortbyref.Pl Error
exome gatk depth-of-coverage sequencing written 5.7 years ago by pm2013 • 50 • updated 5.0 years ago by Biostar ♦♦ 20
15
votes
1
answer
6.2k
views
14 follow
1
answer
Compute Binned Gc-Normalized Read Counts From Bam File
normalization gc depth-of-coverage written 5.0 years ago by Christian • 2.7k • updated 5.0 years ago by Aaronquinlan ♦ 10k
13
votes
3
answers
4.2k
views
5 follow
3
answers
Depth Needed For First Time Transcriptome Sequencing
depth-of-coverage rna transcriptome written 7.6 years ago by Lynn • 30 • updated 5.3 years ago by Michele Busby • 1.9k
3
votes
5
answers
3.4k
views
7 follow
5
answers
Error When Using Depthofcoverage With An Interval File With Gatk
depth-of-coverage coverage written 6.0 years ago by Mamta • 410 • updated 5.4 years ago by ivivek_ngs • 4.6k
5
votes
2
answers
4.0k
views
2
answers
How To Estimate Sequencing Depth Needed To Fully Capture Metagenomic Data?
illumina metagenomics depth-of-coverage written 6.4 years ago by Pawel Szczesny ♦ 3.2k • updated 5.5 years ago by Biostar ♦♦ 20
7
votes
2
answers
3.2k
views
2
answers
Samtools Depth Stdin ?
depth-of-coverage samtools written 5.6 years ago by Mike Axtell • 240 • updated 5.6 years ago by matted ♦ 7.0k
24
votes
5
answers
3.2k
views
10 follow
5
answers
Simulating Read Depth
reads depth-of-coverage simulation written 5.6 years ago by Zev.Kronenberg ♦ 11k • updated 5.6 years ago by KCC • 3.9k
5
votes
1
answer
3.9k
views
1
answer
Vcf File And Interpretation Of Allelic Depth
vcf depth-of-coverage written 5.7 years ago by C00101 • 0 • updated 5.7 years ago by Gabriel R. • 2.5k
5
votes
1
answer
3.7k
views
5 follow
1
answer
Finding The Number Of Reads Which Support A Variant In Vcf
vcf variant-calling depth-of-coverage sequencing written 5.7 years ago by Luca Beltrame • 210 • updated 5.7 years ago by Chris Miller ♦ 20k
2
votes
2
answers
3.4k
views
2
answers
Getting The Average Coverage From The Coverage Counts At Each Depth.
bedtools depth-of-coverage coverage written 5.8 years ago by Jordan • 1.1k • updated 5.7 years ago by Jorge Amigo ♦ 11k
3
votes
1
answer
2.3k
views
1
answer
Recommendation For Cnv Calling Program Based On Depth Of Coverage From Bam
depth-of-coverage bam cnv written 5.8 years ago by Leszek ♦ 4.0k • updated 5.8 years ago by liangkaiye • 250
0
votes
1
answer
2.2k
views
1
answer
A Question About Samtools And Calculating Depth
depth-of-coverage samtools written 5.8 years ago by Sameet • 290 • updated 5.8 years ago by Ashutosh Pandey ♦ 11k
3
votes
1
answer
2.9k
views
1
answer
How Can I Plot A Region'S Depth As Follow? While Tools Should I Use?
depth-of-coverage plot written 5.9 years ago by siyu • 130 • updated 5.9 years ago by Ashutosh Pandey ♦ 11k
2
votes
5
answers
5.4k
views
5
answers
Contig Incompatibility For Depth Of Coverage Calculations Using Gatk
gatk depth-of-coverage contigs written 6.1 years ago by agatorano • 40
5
votes
1
answer
4.1k
views
1
answer
Visualizing The Outputs Of Gatk/Depthofcoverage
gatk depth-of-coverage visualization coverage written 6.1 years ago by Pierre Lindenbaum ♦ 116k • updated 6.1 years ago by Johan • 830
1
vote
2
answers
2.3k
views
2
answers
Incorporating Raw Read Coverage Per Sample In Merged Vcf
vcf merge depth-of-coverage coverage written 6.3 years ago by Drio • 910
2
votes
1
answer
1.3k
views
1
answer
Displaying Information Regarding The Quality Of The Ensembl Genomes
genome ensembl depth-of-coverage coverage written 6.4 years ago by Anima Mundi • 2.4k • updated 6.4 years ago by Andy Yates • 110
16
votes
5
answers
8.1k
views
9 follow
5
answers
How To Get The Read Depth?
genome read depth-of-coverage sequencing written 6.5 years ago by madkitty • 580 • updated 6.5 years ago by Chris Miller ♦ 20k
1
vote
1
answer
4.0k
views
1
answer
Problems In Running Samtools Mpileup/Depth For Specific Regions
depth-of-coverage samtools mpileup written 6.6 years ago by C Shao • 130
0
votes
1
answer
2.5k
views
1
answer
Sequencing Depth And Mutation Frequency
ion-torrent sequencing depth-of-coverage cancer written 6.7 years ago by Luca Beltrame • 210 • updated 6.6 years ago by JC ♦ 7.4k
4
votes
3
answers
4.1k
views
5 follow
3
answers
Samtools Depth Can Only Have Stdout?
depth-of-coverage samtools output written 6.7 years ago by Chris • 40 • updated 6.7 years ago by Pierre Lindenbaum ♦ 116k
10
votes
1
answer
4.3k
views
1
answer
Samtools Depth And Gaps
depth-of-coverage samtools written 6.9 years ago by Juliofdiaz • 130 • updated 6.9 years ago by Pierre Lindenbaum ♦ 116k
2
votes
2
answers
1.9k
views
2
answers
Sequence Depth Genome
homework depth-of-coverage sequence written 7.7 years ago by Oduro • 0 • updated 7.7 years ago by Boboppie • 520
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