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Comment: Comment: Questions about a bug when transferring cram file to bam file
19 days ago by jkbonfield ★ 1.2k
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1.0k
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Comment: Comment: Questions about a bug when transferring cram file to bam file
4 weeks ago by jkbonfield ★ 1.2k
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383
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Comment: Comment: samtools filtering
5 weeks ago by jkbonfield ★ 1.2k
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0
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207
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Comment: Comment: samflags to removes mapped concordantly >1 times
5 weeks ago by jkbonfield ★ 1.2k
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376
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Comment: Comment: BAM to CRAM and BAM recover with smaller size
6 weeks ago by jkbonfield ★ 1.2k
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1
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618
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Comment: Comment: Any ways of extracting and filtering read sequences from cram files with samtool
9 weeks ago by jkbonfield ★ 1.2k
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0
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702
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Comment: Comment: I am trying to generate a bcf file through samtools mpileup but it taking too lo
9 weeks ago by jkbonfield ★ 1.2k
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1.1k
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Comment: Comment: Where is the index command?
5 months ago by jkbonfield ★ 1.2k
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0
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653
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Comment: Comment: Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coor
6 months ago by jkbonfield ★ 1.2k
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0
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625
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Comment: Comment: [main_samview] fail to read the header from "human_g1k_v37.annotate.fasta".
6 months ago by jkbonfield ★ 1.2k
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745
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Comment: Comment: FASTQ to BAM to CRAM to FASTQ
6 months ago by jkbonfield ★ 1.2k
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1
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862
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Comment: Comment: Question on samtools view with --fast option
6 months ago by jkbonfield ★ 1.2k
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0
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1.6k
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Comment: Comment: What is the correct procedure to generate a consensus bacterial sequence?
7 months ago by jkbonfield ★ 1.2k
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34k
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Comment: Comment: Generating consensus sequence from bam file
8 months ago by jkbonfield ★ 1.2k
1
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1
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749
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Comment: Comment: HTSlib threads when ingesting large bgzipped FASTA
10 months ago by jkbonfield ★ 1.2k
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0
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642
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Comment: Comment: Samtools index and sambamba-depth error?
11 months ago by jkbonfield ★ 1.2k
2
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1.7k
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Comment: Comment: Does running samtools sort in parallel result in unexpected output due to tempor
14 months ago by jkbonfield ★ 1.2k
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1
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1.7k
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Comment: Comment: Error in reference fasta file when indexing with samtools
15 months ago by jkbonfield ★ 1.2k
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0
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1.8k
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Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
16 months ago by jkbonfield ★ 1.2k
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0
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1.5k
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Comment: Comment: Consensus sequence calling with normalisation of indels
17 months ago by jkbonfield ★ 1.2k
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0
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695
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Comment: Comment: Merging CRAM files in a specified genomic interval using an input list
17 months ago by jkbonfield ★ 1.2k
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0
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1.2k
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Comment: Comment: samtools index: Numerical result out of range for both .bai and .csi
18 months ago by jkbonfield ★ 1.2k
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1.0k
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Comment: Comment: SNP calling without bcftools and vcftools
18 months ago by jkbonfield ★ 1.2k
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0
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1.1k
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Comment: Comment: Sort BAM file by read mates
18 months ago by jkbonfield ★ 1.2k
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0
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1.2k
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Comment: Comment: Variant calling lost variant
18 months ago by jkbonfield ★ 1.2k
1
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1
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1.4k
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Comment: Comment: Filter out reads with hidden tags in bam files
21 months ago by jkbonfield ★ 1.2k
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0
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760
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Comment: Comment: Problem with extracting reverse-reverse read pairs
21 months ago by jkbonfield ★ 1.2k
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0
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1.4k
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Comment: Comment: Samtools Error "CIGAR and Query lengths differ" but lengths are the same
21 months ago by jkbonfield ★ 1.2k
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0
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2.1k
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Comment: Comment: Error in indexing .bam files from STAR alignment using SAMtools
22 months ago by jkbonfield ★ 1.2k
3
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0
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1.4k
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Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.2 years ago by jkbonfield ★ 1.2k
0
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0
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1.4k
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Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.2 years ago by jkbonfield ★ 1.2k
0
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0
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3.2k
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Comment: Comment: samtools depth and sambamba depth produce different results
2.2 years ago by jkbonfield ★ 1.2k
0
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1
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1.2k
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Comment: Comment: Errors when compiling older version **samtools**
2.3 years ago by jkbonfield ★ 1.2k
0
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0
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2.1k
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Comment: Comment: How to download and transform BAM.1 files (Original format in SRA)
2.4 years ago by jkbonfield ★ 1.2k
0
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0
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1.1k
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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
0
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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
0
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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
0
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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
2.8 years ago by jkbonfield ★ 1.2k
0
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1
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6.5k
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Comment: Comment: bcftools consensus still returns "Could not parse the header" error
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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4.6k
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Comment: Comment: Installing samtools version 1.12
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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949
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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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4.7k
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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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4.7k
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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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3.9k
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Comment: Comment: samtools/bcftools mpileup -B option: to use it or not in order to reduce the occ
3.1 years ago by jkbonfield ★ 1.2k
0
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0
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1.5k
views
Comment: C: Converting CRAM slices to get a CRAM file
3.4 years ago by jkbonfield ★ 1.2k
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