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0
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Comment: Comment: Samtools mpileup - I'm getting different number of base calls compared to number
2.5 years ago by jkbonfield ★ 1.2k
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0
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2.6k
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Comment: Comment: samtools view not removing unwanted headers
2.5 years ago by jkbonfield ★ 1.2k
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0
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1.2k
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Comment: Comment: Convert VCF file to mpileup
2.6 years ago by jkbonfield ★ 1.2k
0
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1
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2.4k
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Comment: Comment: Using samtools to read a bam file
2.6 years ago by jkbonfield ★ 1.2k
2
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0
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1.2k
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Comment: Comment: not primary alignment flag filtering does not work
2.6 years ago by jkbonfield ★ 1.2k
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0
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2.5k
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Comment: Comment: I am converting the fq.gz. files (which are the results of the mgi study) to bam
2.7 years ago by jkbonfield ★ 1.2k
0
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1
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6.4k
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Comment: Comment: bcftools consensus still returns "Could not parse the header" error
2.7 years ago by jkbonfield ★ 1.2k
2
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1
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3.3k
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Answer: Answer: CRAM to BAM using SAMTOOLS
2.8 years ago by jkbonfield ★ 1.2k
1
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0
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2.8k
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Comment: Comment: Visualiation of samtools depth output in a plot
2.8 years ago by jkbonfield ★ 1.2k
0
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1
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4.5k
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Comment: Comment: Installing samtools version 1.12
2.9 years ago by jkbonfield ★ 1.2k
2
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0
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1.1k
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Answer: Answer: Count the numfer of reads supporting a pattern from a BAM file
2.9 years ago by jkbonfield ★ 1.2k
0
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1
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1.9k
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Comment: Comment: alignement and Variant calling with BWA and samtools
3.0 years ago by jkbonfield ★ 1.2k
0
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0
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942
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Comment: Comment: Pysam and CRAM file
3.0 years ago by jkbonfield ★ 1.2k
1
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0
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4.6k
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Comment: Comment: how to use the samtools filtering expression ?
3.0 years ago by jkbonfield ★ 1.2k
2
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0
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2.8k
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Comment: Comment: Extract reads overlapping a specific region in bam file
3.0 years ago by jkbonfield ★ 1.2k
0
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2
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4.6k
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Comment: Comment: how to use the samtools filtering expression ?
3.0 years ago by jkbonfield ★ 1.2k
3
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1
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4.6k
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Answer: Answer: how to use the samtools filtering expression ?
3.0 years ago by jkbonfield ★ 1.2k
2
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0
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3.9k
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Comment: Comment: samtools/bcftools mpileup -B option: to use it or not in order to reduce the occ
3.0 years ago by jkbonfield ★ 1.2k
8
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1
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3.9k
views
Answer: Answer: samtools/bcftools mpileup -B option: to use it or not in order to reduce the occ
3.0 years ago by jkbonfield ★ 1.2k
2
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0
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3.2k
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Answer: Answer: Samtools sort: too many open files error
3.1 years ago by jkbonfield ★ 1.2k
0
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0
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1.5k
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Comment: C: Converting CRAM slices to get a CRAM file
3.4 years ago by jkbonfield ★ 1.2k
2
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1
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1.5k
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Answer: A: Converting CRAM slices to get a CRAM file
3.4 years ago by jkbonfield ★ 1.2k
1
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2
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7.3k
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Answer: A: filter reads in BAM having a tag
3.4 years ago by jkbonfield ★ 1.2k
1
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1
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1.4k
views
Answer: A: Read name not stored in CRAM file. Is it possible to create new read names for r
3.5 years ago by jkbonfield ★ 1.2k
2
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0
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3.1k
views
Answer: A: What is the difference of output samtools depth and samtools view -c on location
4.2 years ago by jkbonfield ★ 1.2k
1
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0
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2.7k
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Comment: C: file size after sorting the BAM file using samtools
4.2 years ago by jkbonfield ★ 1.2k
0
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0
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1.6k
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Comment: C: Collapsing BAM based on seq and positions
4.2 years ago by jkbonfield ★ 1.2k
0
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0
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11k
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Comment: C: BAM files compression
updated 4.3 years ago by 43k • written 4.3 years ago by ★ 1.2k
2
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0
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11k
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Answer: Answer: BAM files compression
updated 2.8 years ago by 43k • written 4.3 years ago by ★ 1.2k
11
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0
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11k
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Answer: A: What is the difference between mpileup samtools and bcftools?
4.3 years ago by jkbonfield ★ 1.2k
0
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0
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2.5k
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Comment: C: Aligning, Sorting and Converting to bam at the same command - possible?
4.3 years ago by jkbonfield ★ 1.2k
9
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1
reply
13k
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Answer: A: How does samtools markdup works?
4.3 years ago by jkbonfield ★ 1.2k
0
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0
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1.2k
views
Comment: C: Extract all BAM reads that intersect a given region using the BAI index
4.3 years ago by jkbonfield ★ 1.2k
1
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0
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1.7k
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Answer: A: Size of Output BAM file bigger than the SUM Size of Input files after merging wi
4.4 years ago by jkbonfield ★ 1.2k
1
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1
reply
2.4k
views
Comment: C: Failure in extracting reads from bam file due to unknown reference
4.5 years ago by jkbonfield ★ 1.2k
0
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0
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3.3k
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Comment: C: Sampling random reads from BAM files with allowing same reads
4.5 years ago by jkbonfield ★ 1.2k
0
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0
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5.1k
views
Comment: C: Does anybody know how to do a local install of samtools on centos without using
4.5 years ago by jkbonfield ★ 1.2k
1
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1
reply
2.0k
views
Answer: A: How to get chrM chr1 ...chr22 chrX chrY order in my bam file
4.5 years ago by jkbonfield ★ 1.2k
0
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0
replies
1.2k
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Comment: C: Merge bam files
4.6 years ago by jkbonfield ★ 1.2k
1
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0
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15k
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Comment: C: Generating consensus sequence from bam file
4.6 years ago by jkbonfield ★ 1.2k
0
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0
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1.3k
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Comment: C: Counting reads starting at a coordinate in bam file
4.6 years ago by jkbonfield ★ 1.2k
1
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1
reply
15k
views
Comment: C: Generating consensus sequence from bam file
4.6 years ago by jkbonfield ★ 1.2k
1
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0
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1.8k
views
Comment: C: samtools flagstat calculation
4.6 years ago by jkbonfield ★ 1.2k
1
vote
0
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919
views
Comment: C: .bam mpileup mapping quality
4.6 years ago by jkbonfield ★ 1.2k
0
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0
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919
views
Answer: A: .bam mpileup mapping quality
4.6 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
996
views
Answer: A: Consensus sequence from multiple BAM files on a single position
4.6 years ago by jkbonfield ★ 1.2k
1
vote
0
replies
10k
views
Comment: C: What Is Best Current Dna Compression Algorithm?
4.7 years ago by jkbonfield ★ 1.2k
8
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1
reply
3.9k
views
Answer: A: Is it possible to directly convert fastq to CRAM ?
4.8 years ago by jkbonfield ★ 1.2k
4
votes
1
reply
6.0k
views
Answer: A: Issue With CRAM -> BAM -> FASTQ Conversion
4.8 years ago by jkbonfield ★ 1.2k
3
votes
2
replies
2.5k
views
Answer: A: Recovering bam files after unknow deletion in the storage
4.9 years ago by jkbonfield ★ 1.2k
103 results • Page 2 of 3
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