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Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.7 years ago by jkbonfield ★ 1.3k
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3.6k
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Comment: Comment: samtools depth and sambamba depth produce different results
2.7 years ago by jkbonfield ★ 1.3k
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1
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1.4k
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Comment: Comment: Errors when compiling older version **samtools**
2.8 years ago by jkbonfield ★ 1.3k
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1.7k
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Answer: Answer: Samtools flagstat result
2.8 years ago by jkbonfield ★ 1.3k
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2.3k
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Comment: Comment: How to download and transform BAM.1 files (Original format in SRA)
2.9 years ago by jkbonfield ★ 1.3k
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1.4k
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Comment: Comment: Samtools mpileup - I'm getting different number of base calls compared to number
3.0 years ago by jkbonfield ★ 1.3k
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3.0k
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Comment: Comment: samtools view not removing unwanted headers
3.0 years ago by jkbonfield ★ 1.3k
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1.4k
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Comment: Comment: Convert VCF file to mpileup
3.1 years ago by jkbonfield ★ 1.3k
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1
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2.7k
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Comment: Comment: Using samtools to read a bam file
3.1 years ago by jkbonfield ★ 1.3k
2
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1.4k
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Comment: Comment: not primary alignment flag filtering does not work
3.1 years ago by jkbonfield ★ 1.3k
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2.9k
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Comment: Comment: I am converting the fq.gz. files (which are the results of the mgi study) to bam
3.3 years ago by jkbonfield ★ 1.3k
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1
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7.3k
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Comment: Comment: bcftools consensus still returns "Could not parse the header" error
3.3 years ago by jkbonfield ★ 1.3k
2
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1
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4.0k
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Answer: Answer: CRAM to BAM using SAMTOOLS
3.3 years ago by jkbonfield ★ 1.3k
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3.3k
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Comment: Comment: Visualiation of samtools depth output in a plot
3.3 years ago by jkbonfield ★ 1.3k
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1
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5.3k
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Comment: Comment: Installing samtools version 1.12
3.4 years ago by jkbonfield ★ 1.3k
2
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1.3k
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Answer: Answer: Count the numfer of reads supporting a pattern from a BAM file
3.4 years ago by jkbonfield ★ 1.3k
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1
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2.2k
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Comment: Comment: alignement and Variant calling with BWA and samtools
3.5 years ago by jkbonfield ★ 1.3k
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0
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1.1k
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Comment: Comment: Pysam and CRAM file
3.5 years ago by jkbonfield ★ 1.3k
1
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0
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5.4k
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Comment: Comment: how to use the samtools filtering expression ?
3.5 years ago by jkbonfield ★ 1.3k
2
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0
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3.3k
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Comment: Comment: Extract reads overlapping a specific region in bam file
3.5 years ago by jkbonfield ★ 1.3k
0
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2
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5.4k
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Comment: Comment: how to use the samtools filtering expression ?
3.5 years ago by jkbonfield ★ 1.3k
3
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1
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5.4k
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Answer: Answer: how to use the samtools filtering expression ?
3.5 years ago by jkbonfield ★ 1.3k
2
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0
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4.4k
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Comment: Comment: samtools/bcftools mpileup -B option: to use it or not in order to reduce the occ
3.6 years ago by jkbonfield ★ 1.3k
8
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1
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4.4k
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Answer: Answer: samtools/bcftools mpileup -B option: to use it or not in order to reduce the occ
3.6 years ago by jkbonfield ★ 1.3k
2
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0
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3.8k
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Answer: Answer: Samtools sort: too many open files error
3.6 years ago by jkbonfield ★ 1.3k
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0
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1.6k
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Comment: C: Converting CRAM slices to get a CRAM file
3.9 years ago by jkbonfield ★ 1.3k
2
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1
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1.6k
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Answer: A: Converting CRAM slices to get a CRAM file
3.9 years ago by jkbonfield ★ 1.3k
1
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2
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8.8k
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Answer: A: filter reads in BAM having a tag
4.0 years ago by jkbonfield ★ 1.3k
1
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1
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1.6k
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Answer: A: Read name not stored in CRAM file. Is it possible to create new read names for r
4.0 years ago by jkbonfield ★ 1.3k
2
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0
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3.3k
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Answer: A: What is the difference of output samtools depth and samtools view -c on location
4.7 years ago by jkbonfield ★ 1.3k
1
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3.3k
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Comment: C: file size after sorting the BAM file using samtools
4.7 years ago by jkbonfield ★ 1.3k
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1.8k
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Comment: C: Collapsing BAM based on seq and positions
4.8 years ago by jkbonfield ★ 1.3k
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Comment: C: BAM files compression
updated 4.8 years ago by 44k • written 4.8 years ago by ★ 1.3k
2
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0
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13k
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Answer: Answer: BAM files compression
updated 3.3 years ago by 44k • written 4.8 years ago by ★ 1.3k
11
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13k
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Answer: A: What is the difference between mpileup samtools and bcftools?
4.8 years ago by jkbonfield ★ 1.3k
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0
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2.8k
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Comment: C: Aligning, Sorting and Converting to bam at the same command - possible?
4.8 years ago by jkbonfield ★ 1.3k
9
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1
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14k
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Answer: A: How does samtools markdup works?
4.9 years ago by jkbonfield ★ 1.3k
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1.3k
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Comment: C: Extract all BAM reads that intersect a given region using the BAI index
4.9 years ago by jkbonfield ★ 1.3k
1
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0
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1.9k
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Answer: A: Size of Output BAM file bigger than the SUM Size of Input files after merging wi
5.0 years ago by jkbonfield ★ 1.3k
1
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1
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2.7k
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Comment: C: Failure in extracting reads from bam file due to unknown reference
5.0 years ago by jkbonfield ★ 1.3k
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0
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3.6k
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Comment: C: Sampling random reads from BAM files with allowing same reads
5.0 years ago by jkbonfield ★ 1.3k
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0
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5.5k
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Comment: C: Does anybody know how to do a local install of samtools on centos without using
5.1 years ago by jkbonfield ★ 1.3k
1
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1
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2.3k
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Answer: A: How to get chrM chr1 ...chr22 chrX chrY order in my bam file
5.1 years ago by jkbonfield ★ 1.3k
0
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0
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1.3k
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Comment: C: Merge bam files
5.2 years ago by jkbonfield ★ 1.3k
1
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17k
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Comment: C: Generating consensus sequence from bam file
5.2 years ago by jkbonfield ★ 1.3k
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0
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1.4k
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Comment: C: Counting reads starting at a coordinate in bam file
5.2 years ago by jkbonfield ★ 1.3k
1
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1
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17k
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Comment: C: Generating consensus sequence from bam file
5.2 years ago by jkbonfield ★ 1.3k
1
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0
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1.9k
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Comment: C: samtools flagstat calculation
5.2 years ago by jkbonfield ★ 1.3k
1
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0
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1.0k
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Comment: C: .bam mpileup mapping quality
5.2 years ago by jkbonfield ★ 1.3k
0
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0
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1.0k
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Answer: A: .bam mpileup mapping quality
5.2 years ago by jkbonfield ★ 1.3k
108 results • Page 2 of 3
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