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744
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Comment: Comment: Questions about a bug when transferring cram file to bam file
8 days ago by jkbonfield ★ 1.2k
0
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0
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340
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Comment: Comment: samtools filtering
15 days ago by jkbonfield ★ 1.2k
0
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0
replies
184
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Comment: Comment: samflags to removes mapped concordantly >1 times
15 days ago by jkbonfield ★ 1.2k
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0
replies
327
views
Comment: Comment: BAM to CRAM and BAM recover with smaller size
23 days ago by jkbonfield ★ 1.2k
0
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1
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553
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Comment: Comment: Any ways of extracting and filtering read sequences from cram files with samtool
6 weeks ago by jkbonfield ★ 1.2k
1
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0
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669
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Comment: Comment: I am trying to generate a bcf file through samtools mpileup but it taking too lo
6 weeks ago by jkbonfield ★ 1.2k
1
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0
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15k
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Answer: Answer: Generating consensus sequence from bam file
6 weeks ago by jkbonfield ★ 1.2k
0
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0
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1.0k
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Comment: Comment: Where is the index command?
4 months ago by jkbonfield ★ 1.2k
0
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0
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622
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Comment: Comment: Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coor
5 months ago by jkbonfield ★ 1.2k
0
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0
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588
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Comment: Comment: [main_samview] fail to read the header from "human_g1k_v37.annotate.fasta".
5 months ago by jkbonfield ★ 1.2k
1
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0
replies
680
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Comment: Comment: FASTQ to BAM to CRAM to FASTQ
6 months ago by jkbonfield ★ 1.2k
0
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1
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784
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Comment: Comment: Question on samtools view with --fast option
6 months ago by jkbonfield ★ 1.2k
1
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0
replies
1.5k
views
Comment: Comment: What is the correct procedure to generate a consensus bacterial sequence?
6 months ago by jkbonfield ★ 1.2k
1
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0
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34k
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Comment: Comment: Generating consensus sequence from bam file
7 months ago by jkbonfield ★ 1.2k
1
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0
replies
1.2k
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Answer: Answer: Merging CRAM files
10 months ago by jkbonfield ★ 1.2k
2
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1
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1.1k
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Answer: Answer: Filter bam file based on cigar string?
10 months ago by jkbonfield ★ 1.2k
0
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1
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34k
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Answer: Answer: Generating consensus sequence from bam file
10 months ago by jkbonfield ★ 1.2k
1
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1
reply
727
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Comment: Comment: HTSlib threads when ingesting large bgzipped FASTA
10 months ago by jkbonfield ★ 1.2k
0
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0
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622
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Comment: Comment: Samtools index and sambamba-depth error?
10 months ago by jkbonfield ★ 1.2k
0
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0
replies
898
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Answer: Answer: Problem generating a .vcf after upgrade of samtools and bcftools
12 months ago by jkbonfield ★ 1.2k
1
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0
replies
1.5k
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Answer: Answer: sam.gz files to bam using samtools
13 months ago by jkbonfield ★ 1.2k
2
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0
replies
1.6k
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Comment: Comment: Does running samtools sort in parallel result in unexpected output due to tempor
13 months ago by jkbonfield ★ 1.2k
1
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1
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996
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Answer: Answer: reference for freebayes or samtools mpileup after extracting chromosome from ali
13 months ago by jkbonfield ★ 1.2k
0
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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
0
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0
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1.7k
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Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
15 months ago by jkbonfield ★ 1.2k
2
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1
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1.4k
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Answer: Answer: samtools calmd and original base quality
15 months ago by jkbonfield ★ 1.2k
1
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0
replies
2.6k
views
Answer: Answer: samtools sort operation very slow, bottle-neck is external hard drive?
15 months ago by jkbonfield ★ 1.2k
0
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0
replies
1.5k
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Comment: Comment: Consensus sequence calling with normalisation of indels
16 months ago by jkbonfield ★ 1.2k
4
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1
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1.2k
views
Answer: Answer: Samtools equivalent of "CleanSam" Picard GATK?
16 months ago by jkbonfield ★ 1.2k
0
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0
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664
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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
0
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0
replies
1.1k
views
Comment: Comment: samtools index: Numerical result out of range for both .bai and .csi
17 months ago by jkbonfield ★ 1.2k
0
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0
replies
1.0k
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Comment: Comment: SNP calling without bcftools and vcftools
17 months ago by jkbonfield ★ 1.2k
1
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0
replies
1.1k
views
Comment: Comment: Sort BAM file by read mates
17 months ago by jkbonfield ★ 1.2k
1
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0
replies
1.2k
views
Comment: Comment: Variant calling lost variant
18 months ago by jkbonfield ★ 1.2k
4
votes
1
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724
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Answer: Answer: Indexing a BAM file without read names
19 months ago by jkbonfield ★ 1.2k
1
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1
reply
1.3k
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Comment: Comment: Filter out reads with hidden tags in bam files
20 months ago by jkbonfield ★ 1.2k
0
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0
replies
738
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Comment: Comment: Problem with extracting reverse-reverse read pairs
20 months ago by jkbonfield ★ 1.2k
1
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1
reply
1.7k
views
Answer: Answer: How to properly pass from samtools rmdup to samtools markdup
20 months ago by jkbonfield ★ 1.2k
0
votes
1
reply
1.7k
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Answer: Answer: How to obtain fasta sequences at only mapped sites
20 months ago by jkbonfield ★ 1.2k
0
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0
replies
1.3k
views
Comment: Comment: Samtools Error "CIGAR and Query lengths differ" but lengths are the same
21 months ago by jkbonfield ★ 1.2k
3
votes
1
reply
1.3k
views
Answer: Answer: Samtools mean depth and max depth results are discordant
21 months ago by jkbonfield ★ 1.2k
0
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0
replies
2.0k
views
Comment: Comment: Error in indexing .bam files from STAR alignment using SAMtools
21 months ago by jkbonfield ★ 1.2k
1
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2
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1.7k
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Answer: Answer: Samtools merge/ "The File BAM exists" warning
21 months ago by jkbonfield ★ 1.2k
3
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0
replies
1.4k
views
Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.1 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.4k
views
Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.1 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
3.2k
views
Comment: Comment: samtools depth and sambamba depth produce different results
2.1 years ago by jkbonfield ★ 1.2k
0
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1
reply
1.2k
views
Comment: Comment: Errors when compiling older version **samtools**
2.2 years ago by jkbonfield ★ 1.2k
0
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0
replies
1.3k
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Answer: Answer: Samtools flagstat result
2.2 years ago by jkbonfield ★ 1.2k
0
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0
replies
2.0k
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Comment: Comment: How to download and transform BAM.1 files (Original format in SRA)
2.3 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.1k
views
Comment: Comment: Samtools mpileup - I'm getting different number of base calls compared to number
2.5 years ago by jkbonfield ★ 1.2k
102 results • Page 1 of 3
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