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Comment: Comment: Removing indels in VCF file
13 months ago by James Reeve ▴ 130
3
votes
12
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5.9k
views
samtools mpileup keeps making an empty file
samtools pileup
updated 20 months ago by ▴ 120 • written 6.8 years ago by ▴ 130
0
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1
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3.7k
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Comment: Comment: Discussion: Uploading terabytes of data to NCBI SRA
2.2 years ago by James Reeve ▴ 130
3
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4
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3.7k
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Forum: Discussion: Uploading terabytes of data to NCBI SRA
NCBI WGS archiving servers remote
updated 2.2 years ago by 154k • written 2.2 years ago by ▴ 130
0
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0
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1.2k
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Comment: Comment: Merged BAM has more reads than sum of parts
2.6 years ago by James Reeve ▴ 130
2
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3
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1.2k
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Merged BAM has more reads than sum of parts
fastq WGS samtools BWA
2.6 years ago by James Reeve ▴ 130
0
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1
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1.3k
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Comment: Comment: Can you predict the size of a BAM file based on the fasta?
4.4 years ago by James Reeve ▴ 130
0
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3
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1.3k
views
Can you predict the size of a BAM file based on the fasta?
storage mapping bam
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 130
0
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0
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9.0k
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Comment: C: Calculate Fis (inbreeding coefficient)
6.4 years ago by James Reeve ▴ 130
0
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0
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1.6k
views
PopGenome: What's the difference between two ways of checking population?
popgenome R
updated 6.4 years ago by 20 • written 6.4 years ago by ▴ 130
1
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1
reply
1.3k
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How do I multithread PoPoolation?
PoPoolation optimization
6.5 years ago by James Reeve ▴ 130
0
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1
reply
2.4k
views
Comment: C: What is the GMAP GFF3 score?
6.6 years ago by James Reeve ▴ 130
0
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3
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2.4k
views
What is the GMAP GFF3 score?
gmap gff3
6.6 years ago by James Reeve ▴ 130
0
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1
reply
41k
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Comment: C: extract only geneID and gene symbol from GTF file
6.7 years ago by James Reeve ▴ 130
0
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0
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3.0k
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Comment: C: Question: Is samtools BAQ redundant after GATK's IndelRealinger
6.7 years ago by James Reeve ▴ 130
0
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1
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3.0k
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Comment: C: Question: Is samtools BAQ redundant after GATK's IndelRealinger
6.7 years ago by James Reeve ▴ 130
4
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5
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3.0k
views
Question: Is samtools BAQ redundant after GATK's IndelRealinger
samtools indels
6.7 years ago by James Reeve ▴ 130
2
votes
2
replies
2.9k
views
VarScan: How is the DP score in a .vcf calculated?
VarScan VCF
updated 6.8 years ago by 13k • written 6.8 years ago by ▴ 130
0
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0
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5.9k
views
Comment: C: samtools mpileup keeps making an empty file
6.8 years ago by James Reeve ▴ 130
0
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1
reply
5.9k
views
Comment: C: samtools mpileup keeps making an empty file
6.8 years ago by James Reeve ▴ 130
0
votes
1
reply
5.9k
views
Comment: C: samtools mpileup keeps making an empty file
6.8 years ago by James Reeve ▴ 130
0
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0
replies
5.9k
views
Comment: C: samtools mpileup keeps making an empty file
6.8 years ago by James Reeve ▴ 130
0
votes
0
replies
5.9k
views
Comment: C: samtools mpileup keeps making an empty file
6.8 years ago by James Reeve ▴ 130
0
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0
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3.2k
views
Comment: C: Can I get AddOrReplaceReadGroups working for multiple files?
7.0 years ago by James Reeve ▴ 130
4
votes
3
replies
3.2k
views
Can I get AddOrReplaceReadGroups working for multiple files?
picard tools bash
updated 7.0 years ago by ★ 1.4k • written 7.0 years ago by ▴ 130
1
vote
1
reply
4.6k
views
How do I chose variant quality filters for a VCF file?
snp variant filter
7.2 years ago by James Reeve ▴ 130
1
vote
1
reply
6.0k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
7.2 years ago by James Reeve ▴ 130
0
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0
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6.0k
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Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
7.2 years ago by James Reeve ▴ 130
0
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1
reply
6.0k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
7.2 years ago by James Reeve ▴ 130
0
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0
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6.0k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
7.2 years ago by James Reeve ▴ 130
0
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1
reply
6.0k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
7.2 years ago by James Reeve ▴ 130
0
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1
reply
6.0k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
7.2 years ago by James Reeve ▴ 130
2
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14
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6.0k
views
Error: Help understand Trimmomatic ZLIB input stream error
Trimmomatic
7.2 years ago by James Reeve ▴ 130
0
votes
0
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2.0k
views
How do you get multi-allelic SNP calls form a pooled sequence using GATK?
GATK SNPcalling multi-allelic_snp
7.3 years ago by James Reeve ▴ 130
0
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1
reply
4.3k
views
Comment: C: Locating Multiple Alternate Alleles in gatk.vcf file
7.3 years ago by James Reeve ▴ 130
0
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0
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3.7k
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Comment: C: GATK SNPs calling multiple sample without any known SNPs database
7.4 years ago by James Reeve ▴ 130
0
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1
reply
2.2k
views
Comment: C: Does SortSam lead to a loss of data?
7.4 years ago by James Reeve ▴ 130
0
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1
reply
2.2k
views
Comment: C: Does SortSam lead to a loss of data?
7.4 years ago by James Reeve ▴ 130
3
votes
5
replies
2.2k
views
Does SortSam lead to a loss of data?
Picard
updated 7.4 years ago by 90k • written 7.4 years ago by ▴ 130
0
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1
reply
4.1k
views
Comment: C: Can someone explain what the -M option in BWA-MEM does?
7.4 years ago by James Reeve ▴ 130
3
votes
4
replies
4.1k
views
Can someone explain what the -M option in BWA-MEM does?
BWA alignment
updated 7.4 years ago by 105k • written 7.4 years ago by ▴ 130
0
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1
reply
4.8k
views
Comment: C: BQSR vs VQSR
7.4 years ago by James Reeve ▴ 130
4
votes
3
replies
4.8k
views
BQSR vs VQSR
SNP GATK
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 130
31
votes
4
replies
10k
views
Genotyping, genotype calling or SNP calling?
SNP alignment
updated 8.1 years ago by 89k • written 8.1 years ago by ▴ 130
0
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1
reply
5.3k
views
Comment: C: determining appropriate window size for identifying highly differentiated SNPs
8.1 years ago by James Reeve ▴ 130
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