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Comment: Comment: Removing indels in VCF file
10 weeks ago by James Reeve ▴ 130
3
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12
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4.8k
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samtools mpileup keeps making an empty file
samtools pileup
updated 9 months ago by ▴ 120 • written 5.9 years ago by ▴ 130
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1
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2.0k
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Comment: Comment: Discussion: Uploading terabytes of data to NCBI SRA
15 months ago by James Reeve ▴ 130
3
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4
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2.0k
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Forum: Discussion: Uploading terabytes of data to NCBI SRA
NCBI WGS archiving servers remote
updated 15 months ago by 148k • written 15 months ago by ▴ 130
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743
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Comment: Comment: Merged BAM has more reads than sum of parts
20 months ago by James Reeve ▴ 130
2
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3
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743
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Merged BAM has more reads than sum of parts
fastq WGS samtools BWA
20 months ago by James Reeve ▴ 130
0
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1
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998
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Comment: Comment: Can you predict the size of a BAM file based on the fasta?
3.5 years ago by James Reeve ▴ 130
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3
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998
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Can you predict the size of a BAM file based on the fasta?
storage mapping bam
updated 3.5 years ago by 88k • written 3.5 years ago by ▴ 130
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0
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7.6k
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Comment: C: Calculate Fis (inbreeding coefficient)
5.4 years ago by James Reeve ▴ 130
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0
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1.4k
views
PopGenome: What's the difference between two ways of checking population?
popgenome R
updated 5.4 years ago by 20 • written 5.5 years ago by ▴ 130
1
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1
reply
1.1k
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How do I multithread PoPoolation?
PoPoolation optimization
5.6 years ago by James Reeve ▴ 130
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1
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2.0k
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Comment: C: What is the GMAP GFF3 score?
5.7 years ago by James Reeve ▴ 130
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3
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2.0k
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What is the GMAP GFF3 score?
gmap gff3
5.7 years ago by James Reeve ▴ 130
0
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1
reply
36k
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Comment: C: extract only geneID and gene symbol from GTF file
5.8 years ago by James Reeve ▴ 130
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0
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2.5k
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Comment: C: Question: Is samtools BAQ redundant after GATK's IndelRealinger
5.8 years ago by James Reeve ▴ 130
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1
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2.5k
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Comment: C: Question: Is samtools BAQ redundant after GATK's IndelRealinger
5.8 years ago by James Reeve ▴ 130
4
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5
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2.5k
views
Question: Is samtools BAQ redundant after GATK's IndelRealinger
samtools indels
5.8 years ago by James Reeve ▴ 130
2
votes
2
replies
2.4k
views
VarScan: How is the DP score in a .vcf calculated?
VarScan VCF
updated 5.9 years ago by 13k • written 5.9 years ago by ▴ 130
0
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0
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4.8k
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Comment: C: samtools mpileup keeps making an empty file
5.9 years ago by James Reeve ▴ 130
0
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1
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4.8k
views
Comment: C: samtools mpileup keeps making an empty file
5.9 years ago by James Reeve ▴ 130
0
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1
reply
4.8k
views
Comment: C: samtools mpileup keeps making an empty file
5.9 years ago by James Reeve ▴ 130
0
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0
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4.8k
views
Comment: C: samtools mpileup keeps making an empty file
5.9 years ago by James Reeve ▴ 130
0
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0
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4.8k
views
Comment: C: samtools mpileup keeps making an empty file
5.9 years ago by James Reeve ▴ 130
0
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0
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2.6k
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Comment: C: Can I get AddOrReplaceReadGroups working for multiple files?
6.1 years ago by James Reeve ▴ 130
4
votes
3
replies
2.6k
views
Can I get AddOrReplaceReadGroups working for multiple files?
picard tools bash
updated 6.1 years ago by ★ 1.3k • written 6.1 years ago by ▴ 130
1
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1
reply
4.4k
views
How do I chose variant quality filters for a VCF file?
snp variant filter
6.3 years ago by James Reeve ▴ 130
1
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1
reply
5.1k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
6.3 years ago by James Reeve ▴ 130
0
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0
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5.1k
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Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
6.3 years ago by James Reeve ▴ 130
0
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1
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5.1k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
6.3 years ago by James Reeve ▴ 130
0
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0
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5.1k
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Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
6.3 years ago by James Reeve ▴ 130
0
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1
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5.1k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
6.3 years ago by James Reeve ▴ 130
0
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1
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5.1k
views
Comment: C: Error: Help understand Trimmomatic ZLIB input stream error
6.3 years ago by James Reeve ▴ 130
2
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14
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5.1k
views
Error: Help understand Trimmomatic ZLIB input stream error
Trimmomatic
6.3 years ago by James Reeve ▴ 130
0
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0
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1.8k
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How do you get multi-allelic SNP calls form a pooled sequence using GATK?
GATK SNPcalling multi-allelic_snp
6.4 years ago by James Reeve ▴ 130
0
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1
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3.4k
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Comment: C: Locating Multiple Alternate Alleles in gatk.vcf file
6.4 years ago by James Reeve ▴ 130
0
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0
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3.1k
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Comment: C: GATK SNPs calling multiple sample without any known SNPs database
6.4 years ago by James Reeve ▴ 130
0
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1
reply
1.7k
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Comment: C: Does SortSam lead to a loss of data?
6.5 years ago by James Reeve ▴ 130
0
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1
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1.7k
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Comment: C: Does SortSam lead to a loss of data?
6.5 years ago by James Reeve ▴ 130
3
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5
replies
1.7k
views
Does SortSam lead to a loss of data?
Picard
updated 6.5 years ago by 86k • written 6.5 years ago by ▴ 130
0
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1
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3.2k
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Comment: C: Can someone explain what the -M option in BWA-MEM does?
6.5 years ago by James Reeve ▴ 130
3
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4
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3.2k
views
Can someone explain what the -M option in BWA-MEM does?
BWA alignment
updated 6.5 years ago by 104k • written 6.5 years ago by ▴ 130
0
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1
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4.1k
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Comment: C: BQSR vs VQSR
6.5 years ago by James Reeve ▴ 130
4
votes
3
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4.1k
views
BQSR vs VQSR
SNP GATK
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 130
31
votes
4
replies
9.5k
views
Genotyping, genotype calling or SNP calling?
SNP alignment
updated 7.2 years ago by 88k • written 7.2 years ago by ▴ 130
0
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1
reply
4.5k
views
Comment: C: determining appropriate window size for identifying highly differentiated SNPs
7.2 years ago by James Reeve ▴ 130
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