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820
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Answer: Answer: How to create a consensus of a contig with samtools or bbmap?
19 days ago by jkbonfield ★ 1.3k
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0
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1.5k
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Answer: Answer: Modify read groups in BAM file
5 months ago by jkbonfield ★ 1.3k
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0
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1.3k
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Comment: Comment: ERROR: SAM file generated by BWA is corrupted and cannot be processed with SAMTO
8 months ago by jkbonfield ★ 1.3k
1
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0
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1.2k
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Comment: Comment: Should we cite sed / awk in papers?
8 months ago by jkbonfield ★ 1.3k
1
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1
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1.8k
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Answer: Answer: Parsing error in sam file when converting to bam
9 months ago by jkbonfield ★ 1.3k
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0
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1.3k
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Comment: Comment: Extracting CDS Region of FFAR4 Gene Using Samtools from GRCh38 Reference Genome
9 months ago by jkbonfield ★ 1.3k
1
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0
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952
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Answer: Answer: Creating CRC32 hashes in a CRAM file header
11 months ago by jkbonfield ★ 1.3k
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0
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4.0k
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Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
13 months ago by jkbonfield ★ 1.3k
0
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0
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46k
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Comment: Comment: Generating consensus sequence from bam file
13 months ago by jkbonfield ★ 1.3k
1
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1
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2.2k
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Comment: Comment: Need to split a cram file into smaller pieces - how to extract and save cram for
14 months ago by jkbonfield ★ 1.3k
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0
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2.2k
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Answer: Answer: Need to split a cram file into smaller pieces - how to extract and save cram for
14 months ago by jkbonfield ★ 1.3k
2
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0
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1.6k
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Answer: Answer: filter reads based on mapped length
updated 16 months ago by 3.1k • written 16 months ago by ★ 1.3k
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0
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2.6k
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Comment: Comment: Questions about a bug when transferring cram file to bam file
18 months ago by jkbonfield ★ 1.3k
1
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1
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2.6k
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Comment: Comment: Questions about a bug when transferring cram file to bam file
18 months ago by jkbonfield ★ 1.3k
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0
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1.2k
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Comment: Comment: samtools filtering
19 months ago by jkbonfield ★ 1.3k
0
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0
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601
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Comment: Comment: samflags to removes mapped concordantly >1 times
19 months ago by jkbonfield ★ 1.3k
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0
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1.1k
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Comment: Comment: BAM to CRAM and BAM recover with smaller size
19 months ago by jkbonfield ★ 1.3k
0
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1
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2.7k
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Comment: Comment: Any ways of extracting and filtering read sequences from cram files with samtool
19 months ago by jkbonfield ★ 1.3k
1
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0
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1.8k
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Comment: Comment: I am trying to generate a bcf file through samtools mpileup but it taking too lo
19 months ago by jkbonfield ★ 1.3k
2
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1
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22k
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Answer: Answer: Generating consensus sequence from bam file
19 months ago by jkbonfield ★ 1.3k
0
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0
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2.3k
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Comment: Comment: Where is the index command?
23 months ago by jkbonfield ★ 1.3k
0
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0
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1.3k
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Comment: Comment: Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coor
23 months ago by jkbonfield ★ 1.3k
0
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0
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1.4k
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Comment: Comment: [main_samview] fail to read the header from "human_g1k_v37.annotate.fasta".
23 months ago by jkbonfield ★ 1.3k
1
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0
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1.7k
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Comment: Comment: FASTQ to BAM to CRAM to FASTQ
2.0 years ago by jkbonfield ★ 1.3k
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1
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2.9k
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Comment: Comment: Question on samtools view with --fast option
2.0 years ago by jkbonfield ★ 1.3k
1
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0
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5.2k
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Comment: Comment: What is the correct procedure to generate a consensus bacterial sequence?
2.0 years ago by jkbonfield ★ 1.3k
1
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0
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46k
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Comment: Comment: Generating consensus sequence from bam file
2.1 years ago by jkbonfield ★ 1.3k
2
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0
replies
2.9k
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Answer: Answer: Merging CRAM files
2.4 years ago by jkbonfield ★ 1.3k
2
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1
reply
2.0k
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Answer: Answer: Filter bam file based on cigar string?
2.4 years ago by jkbonfield ★ 1.3k
2
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2
replies
46k
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Answer: Answer: Generating consensus sequence from bam file
2.4 years ago by jkbonfield ★ 1.3k
1
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1
reply
2.1k
views
Comment: Comment: HTSlib threads when ingesting large bgzipped FASTA
2.4 years ago by jkbonfield ★ 1.3k
0
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0
replies
1.2k
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Comment: Comment: Samtools index and sambamba-depth error?
2.4 years ago by jkbonfield ★ 1.3k
0
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0
replies
2.0k
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Answer: Answer: Problem generating a .vcf after upgrade of samtools and bcftools
2.6 years ago by jkbonfield ★ 1.3k
1
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0
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3.2k
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Answer: Answer: sam.gz files to bam using samtools
2.7 years ago by jkbonfield ★ 1.3k
2
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0
replies
3.0k
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Comment: Comment: Does running samtools sort in parallel result in unexpected output due to tempor
2.7 years ago by jkbonfield ★ 1.3k
1
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1
reply
1.8k
views
Answer: Answer: reference for freebayes or samtools mpileup after extracting chromosome from ali
2.7 years ago by jkbonfield ★ 1.3k
0
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1
reply
3.4k
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Comment: Comment: Error in reference fasta file when indexing with samtools
2.8 years ago by jkbonfield ★ 1.3k
0
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0
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4.0k
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Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
2.8 years ago by jkbonfield ★ 1.3k
2
votes
1
reply
2.9k
views
Answer: Answer: samtools calmd and original base quality
2.8 years ago by jkbonfield ★ 1.3k
1
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0
replies
6.5k
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Answer: Answer: samtools sort operation very slow, bottle-neck is external hard drive?
2.8 years ago by jkbonfield ★ 1.3k
0
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0
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2.8k
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Comment: Comment: Consensus sequence calling with normalisation of indels
2.9 years ago by jkbonfield ★ 1.3k
4
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1
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2.1k
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Answer: Answer: Samtools equivalent of "CleanSam" Picard GATK?
2.9 years ago by jkbonfield ★ 1.3k
0
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0
replies
1.2k
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Comment: Comment: Merging CRAM files in a specified genomic interval using an input list
2.9 years ago by jkbonfield ★ 1.3k
0
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0
replies
2.9k
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Comment: Comment: samtools index: Numerical result out of range for both .bai and .csi
2.9 years ago by jkbonfield ★ 1.3k
0
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0
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1.8k
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Comment: Comment: SNP calling without bcftools and vcftools
2.9 years ago by jkbonfield ★ 1.3k
1
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0
replies
1.9k
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Comment: Comment: Sort BAM file by read mates
3.0 years ago by jkbonfield ★ 1.3k
1
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0
replies
2.2k
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Comment: Comment: Variant calling lost variant
3.0 years ago by jkbonfield ★ 1.3k
4
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1
reply
1.3k
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Answer: Answer: Indexing a BAM file without read names
3.1 years ago by jkbonfield ★ 1.3k
1
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1
reply
2.8k
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Comment: Comment: Filter out reads with hidden tags in bam files
3.2 years ago by jkbonfield ★ 1.3k
0
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0
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1.4k
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Comment: Comment: Problem with extracting reverse-reverse read pairs
3.2 years ago by jkbonfield ★ 1.3k
115 results • Page 1 of 3
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