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938
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Comment:
Comment: Questions about a bug when transferring cram file to bam file
9 days ago by
jkbonfield
★ 1.2k
1
vote
1
reply
938
views
Comment:
Comment: Questions about a bug when transferring cram file to bam file
20 days ago by
jkbonfield
★ 1.2k
0
votes
0
replies
367
views
Comment:
Comment: samtools filtering
27 days ago by
jkbonfield
★ 1.2k
0
votes
0
replies
198
views
Comment:
Comment: samflags to removes mapped concordantly >1 times
27 days ago by
jkbonfield
★ 1.2k
0
votes
0
replies
353
views
Comment:
Comment: BAM to CRAM and BAM recover with smaller size
5 weeks ago by
jkbonfield
★ 1.2k
0
votes
1
reply
590
views
Comment:
Comment: Any ways of extracting and filtering read sequences from cram files with samtool
7 weeks ago by
jkbonfield
★ 1.2k
1
vote
0
replies
689
views
Comment:
Comment: I am trying to generate a bcf file through samtools mpileup but it taking too lo
7 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
636
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
608
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
711
views
Comment:
Comment: FASTQ to BAM to CRAM to FASTQ
6 months ago by
jkbonfield
★ 1.2k
0
votes
1
reply
824
views
Comment:
Comment: Question on samtools view with --fast option
6 months ago by
jkbonfield
★ 1.2k
1
vote
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
vote
0
replies
34k
views
Comment:
Comment: Generating consensus sequence from bam file
7 months ago by
jkbonfield
★ 1.2k
1
vote
1
reply
743
views
Comment:
Comment: HTSlib threads when ingesting large bgzipped FASTA
10 months ago by
jkbonfield
★ 1.2k
0
votes
0
replies
637
views
Comment:
Comment: Samtools index and sambamba-depth error?
11 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
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?
15 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
0
votes
0
replies
679
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
17 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
1
vote
1
reply
1.4k
views
Comment:
Comment: Filter out reads with hidden tags in bam files
20 months ago by
jkbonfield
★ 1.2k
0
votes
0
replies
750
views
Comment:
Comment: Problem with extracting reverse-reverse read pairs
20 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
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
3
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
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
2.2 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
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
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
0
votes
0
replies
2.6k
views
Comment:
Comment: samtools view not removing unwanted headers
2.5 years ago by
jkbonfield
★ 1.2k
0
votes
0
replies
1.2k
views
Comment:
Comment: Convert VCF file to mpileup
2.6 years ago by
jkbonfield
★ 1.2k
0
votes
1
reply
2.4k
views
Comment:
Comment: Using samtools to read a bam file
2.6 years ago by
jkbonfield
★ 1.2k
2
votes
0
replies
1.2k
views
Comment:
Comment: not primary alignment flag filtering does not work
2.6 years ago by
jkbonfield
★ 1.2k
0
votes
0
replies
2.5k
views
Comment:
Comment: I am converting the fq.gz. files (which are the results of the mgi study) to bam
2.7 years ago by
jkbonfield
★ 1.2k
0
votes
1
reply
6.4k
views
Comment:
Comment: bcftools consensus still returns "Could not parse the header" error
2.7 years ago by
jkbonfield
★ 1.2k
1
vote
0
replies
2.8k
views
Comment:
Comment: Visualiation of samtools depth output in a plot
2.8 years ago by
jkbonfield
★ 1.2k
0
votes
1
reply
4.5k
views
Comment:
Comment: Installing samtools version 1.12
2.9 years ago by
jkbonfield
★ 1.2k
0
votes
1
reply
1.9k
views
Comment:
Comment: alignement and Variant calling with BWA and samtools
3.0 years ago by
jkbonfield
★ 1.2k
0
votes
0
replies
942
views
Comment:
Comment: Pysam and CRAM file
3.0 years ago by
jkbonfield
★ 1.2k
1
vote
0
replies
4.6k
views
Comment:
Comment: how to use the samtools filtering expression ?
3.0 years ago by
jkbonfield
★ 1.2k
2
votes
0
replies
2.8k
views
Comment:
Comment: Extract reads overlapping a specific region in bam file
3.0 years ago by
jkbonfield
★ 1.2k
0
votes
2
replies
4.6k
views
Comment:
Comment: how to use the samtools filtering expression ?
3.0 years ago by
jkbonfield
★ 1.2k
2
votes
0
replies
3.9k
views
Comment:
Comment: samtools/bcftools mpileup -B option: to use it or not in order to reduce the occ
3.0 years ago by
jkbonfield
★ 1.2k
0
votes
0
replies
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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