Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
0
votes
0
replies
999
views
Comment: Comment: Questions about a bug when transferring cram file to bam file
17 days ago by jkbonfield ★ 1.2k
1
vote
1
reply
999
views
Comment: Comment: Questions about a bug when transferring cram file to bam file
28 days ago by jkbonfield ★ 1.2k
0
votes
0
replies
380
views
Comment: Comment: samtools filtering
5 weeks ago by jkbonfield ★ 1.2k
0
votes
0
replies
206
views
Comment: Comment: samflags to removes mapped concordantly >1 times
5 weeks ago by jkbonfield ★ 1.2k
0
votes
0
replies
373
views
Comment: Comment: BAM to CRAM and BAM recover with smaller size
6 weeks ago by jkbonfield ★ 1.2k
0
votes
1
reply
608
views
Comment: Comment: Any ways of extracting and filtering read sequences from cram files with samtool
9 weeks ago by jkbonfield ★ 1.2k
1
vote
0
replies
701
views
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
1
vote
0
replies
15k
views
Answer: Answer: Generating consensus sequence from bam file
9 weeks ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.0k
views
Comment: Comment: Where is the index command?
5 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
647
views
Comment: Comment: Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coor
5 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
621
views
Comment: Comment: [main_samview] fail to read the header from "human_g1k_v37.annotate.fasta".
5 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
736
views
Comment: Comment: FASTQ to BAM to CRAM to FASTQ
6 months ago by jkbonfield ★ 1.2k
0
votes
1
reply
851
views
Comment: Comment: Question on samtools view with --fast option
6 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
1.6k
views
Comment: Comment: What is the correct procedure to generate a consensus bacterial sequence?
7 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
34k
views
Comment: Comment: Generating consensus sequence from bam file
8 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
1.2k
views
Answer: Answer: Merging CRAM files
10 months ago by jkbonfield ★ 1.2k
2
votes
1
reply
1.1k
views
Answer: Answer: Filter bam file based on cigar string?
10 months ago by jkbonfield ★ 1.2k
0
votes
1
reply
34k
views
Answer: Answer: Generating consensus sequence from bam file
10 months ago by jkbonfield ★ 1.2k
1
vote
1
reply
749
views
Comment: Comment: HTSlib threads when ingesting large bgzipped FASTA
10 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
640
views
Comment: Comment: Samtools index and sambamba-depth error?
11 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
931
views
Answer: Answer: Problem generating a .vcf after upgrade of samtools and bcftools
13 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
1.6k
views
Answer: Answer: sam.gz files to bam using samtools
14 months ago by jkbonfield ★ 1.2k
2
votes
0
replies
1.7k
views
Comment: Comment: Does running samtools sort in parallel result in unexpected output due to tempor
14 months ago by jkbonfield ★ 1.2k
1
vote
1
reply
1.0k
views
Answer: Answer: reference for freebayes or samtools mpileup after extracting chromosome from ali
14 months ago by jkbonfield ★ 1.2k
0
votes
1
reply
1.7k
views
Comment: Comment: Error in reference fasta file when indexing with samtools
15 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.8k
views
Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
16 months ago by jkbonfield ★ 1.2k
2
votes
1
reply
1.5k
views
Answer: Answer: samtools calmd and original base quality
16 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
2.7k
views
Answer: Answer: samtools sort operation very slow, bottle-neck is external hard drive?
16 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.5k
views
Comment: Comment: Consensus sequence calling with normalisation of indels
17 months ago by jkbonfield ★ 1.2k
4
votes
1
reply
1.3k
views
Answer: Answer: Samtools equivalent of "CleanSam" Picard GATK?
17 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
692
views
Comment: Comment: Merging CRAM files in a specified genomic interval using an input list
17 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.2k
views
Comment: Comment: samtools index: Numerical result out of range for both .bai and .csi
17 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.0k
views
Comment: Comment: SNP calling without bcftools and vcftools
17 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
1.1k
views
Comment: Comment: Sort BAM file by read mates
18 months ago by jkbonfield ★ 1.2k
1
vote
0
replies
1.2k
views
Comment: Comment: Variant calling lost variant
18 months ago by jkbonfield ★ 1.2k
4
votes
1
reply
742
views
Answer: Answer: Indexing a BAM file without read names
19 months ago by jkbonfield ★ 1.2k
1
vote
1
reply
1.4k
views
Comment: Comment: Filter out reads with hidden tags in bam files
21 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
758
views
Comment: Comment: Problem with extracting reverse-reverse read pairs
21 months ago by jkbonfield ★ 1.2k
1
vote
1
reply
1.7k
views
Answer: Answer: How to properly pass from samtools rmdup to samtools markdup
21 months ago by jkbonfield ★ 1.2k
0
votes
1
reply
1.8k
views
Answer: Answer: How to obtain fasta sequences at only mapped sites
21 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.4k
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
1.4k
views
Answer: Answer: Samtools mean depth and max depth results are discordant
22 months ago by jkbonfield ★ 1.2k
0
votes
0
replies
2.1k
views
Comment: Comment: Error in indexing .bam files from STAR alignment using SAMtools
22 months ago by jkbonfield ★ 1.2k
1
vote
2
replies
1.7k
views
Answer: Answer: Samtools merge/ "The File BAM exists" warning
22 months ago by jkbonfield ★ 1.2k
3
votes
0
replies
1.4k
views
Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.2 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
2.2 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
3.2k
views
Comment: Comment: samtools depth and sambamba depth produce different results
2.2 years ago by jkbonfield ★ 1.2k
0
votes
1
reply
1.2k
views
Comment: Comment: Errors when compiling older version **samtools**
2.3 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
1.4k
views
Answer: Answer: Samtools flagstat result
2.3 years ago by jkbonfield ★ 1.2k
0
votes
0
replies
2.0k
views
Comment: Comment: How to download and transform BAM.1 files (Original format in SRA)
2.3 years ago by jkbonfield ★ 1.2k
103 results • Page 1 of 3
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6