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Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
9 weeks ago by jkbonfield ★ 1.3k
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39k
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Comment: Comment: Generating consensus sequence from bam file
9 weeks ago by jkbonfield ★ 1.3k
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0
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635
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Comment: Comment: Need to split a cram file into smaller pieces - how to extract and save cram for
3 months ago by jkbonfield ★ 1.3k
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0
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635
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Answer: Answer: Need to split a cram file into smaller pieces - how to extract and save cram for
3 months ago by jkbonfield ★ 1.3k
2
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631
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Answer: Answer: filter reads based on mapped length
updated 4 months ago by 3.1k • written 5 months ago by ★ 1.3k
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1.4k
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Comment: Comment: Questions about a bug when transferring cram file to bam file
6 months ago by jkbonfield ★ 1.3k
1
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1
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1.4k
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Comment: Comment: Questions about a bug when transferring cram file to bam file
7 months ago by jkbonfield ★ 1.3k
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0
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605
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Comment: Comment: samtools filtering
7 months ago by jkbonfield ★ 1.3k
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321
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Comment: Comment: samflags to removes mapped concordantly >1 times
7 months ago by jkbonfield ★ 1.3k
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0
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579
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Comment: Comment: BAM to CRAM and BAM recover with smaller size
7 months ago by jkbonfield ★ 1.3k
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1
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1.2k
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Comment: Comment: Any ways of extracting and filtering read sequences from cram files with samtool
8 months ago by jkbonfield ★ 1.3k
1
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0
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988
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Comment: Comment: I am trying to generate a bcf file through samtools mpileup but it taking too lo
8 months ago by jkbonfield ★ 1.3k
2
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1
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17k
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Answer: Answer: Generating consensus sequence from bam file
8 months ago by jkbonfield ★ 1.3k
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0
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1.3k
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Comment: Comment: Where is the index command?
11 months ago by jkbonfield ★ 1.3k
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848
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Comment: Comment: Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coor
12 months ago by jkbonfield ★ 1.3k
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0
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838
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Comment: Comment: [main_samview] fail to read the header from "human_g1k_v37.annotate.fasta".
12 months ago by jkbonfield ★ 1.3k
1
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0
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1.0k
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Comment: Comment: FASTQ to BAM to CRAM to FASTQ
13 months ago by jkbonfield ★ 1.3k
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1
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1.5k
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Comment: Comment: Question on samtools view with --fast option
13 months ago by jkbonfield ★ 1.3k
1
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0
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2.3k
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Comment: Comment: What is the correct procedure to generate a consensus bacterial sequence?
13 months ago by jkbonfield ★ 1.3k
1
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0
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39k
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Comment: Comment: Generating consensus sequence from bam file
14 months ago by jkbonfield ★ 1.3k
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0
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1.7k
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Answer: Answer: Merging CRAM files
17 months ago by jkbonfield ★ 1.3k
2
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1
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1.4k
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Answer: Answer: Filter bam file based on cigar string?
17 months ago by jkbonfield ★ 1.3k
2
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2
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39k
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Answer: Answer: Generating consensus sequence from bam file
17 months ago by jkbonfield ★ 1.3k
1
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1
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960
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Comment: Comment: HTSlib threads when ingesting large bgzipped FASTA
17 months ago by jkbonfield ★ 1.3k
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0
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794
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Comment: Comment: Samtools index and sambamba-depth error?
17 months ago by jkbonfield ★ 1.3k
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0
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1.2k
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Answer: Answer: Problem generating a .vcf after upgrade of samtools and bcftools
19 months ago by jkbonfield ★ 1.3k
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0
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2.1k
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Answer: Answer: sam.gz files to bam using samtools
20 months ago by jkbonfield ★ 1.3k
2
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0
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2.1k
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Comment: Comment: Does running samtools sort in parallel result in unexpected output due to tempor
20 months ago by jkbonfield ★ 1.3k
1
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1
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1.3k
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Answer: Answer: reference for freebayes or samtools mpileup after extracting chromosome from ali
20 months ago by jkbonfield ★ 1.3k
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1
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2.2k
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Comment: Comment: Error in reference fasta file when indexing with samtools
22 months ago by jkbonfield ★ 1.3k
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0
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2.5k
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Comment: Comment: Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
22 months ago by jkbonfield ★ 1.3k
2
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1
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2.0k
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Answer: Answer: samtools calmd and original base quality
22 months ago by jkbonfield ★ 1.3k
1
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0
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3.6k
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Answer: Answer: samtools sort operation very slow, bottle-neck is external hard drive?
22 months ago by jkbonfield ★ 1.3k
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0
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1.8k
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Comment: Comment: Consensus sequence calling with normalisation of indels
23 months ago by jkbonfield ★ 1.3k
4
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1
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1.5k
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Answer: Answer: Samtools equivalent of "CleanSam" Picard GATK?
23 months ago by jkbonfield ★ 1.3k
0
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0
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808
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Comment: Comment: Merging CRAM files in a specified genomic interval using an input list
24 months ago by jkbonfield ★ 1.3k
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0
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1.6k
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Comment: Comment: samtools index: Numerical result out of range for both .bai and .csi
24 months ago by jkbonfield ★ 1.3k
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0
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1.2k
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Comment: Comment: SNP calling without bcftools and vcftools
24 months ago by jkbonfield ★ 1.3k
1
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0
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1.3k
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Comment: Comment: Sort BAM file by read mates
2.0 years ago by jkbonfield ★ 1.3k
1
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0
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1.4k
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Comment: Comment: Variant calling lost variant
2.1 years ago by jkbonfield ★ 1.3k
4
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1
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892
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Answer: Answer: Indexing a BAM file without read names
2.2 years ago by jkbonfield ★ 1.3k
1
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1
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1.8k
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Comment: Comment: Filter out reads with hidden tags in bam files
2.3 years ago by jkbonfield ★ 1.3k
0
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0
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911
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Comment: Comment: Problem with extracting reverse-reverse read pairs
2.3 years ago by jkbonfield ★ 1.3k
1
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1
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2.2k
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Answer: Answer: How to properly pass from samtools rmdup to samtools markdup
2.3 years ago by jkbonfield ★ 1.3k
0
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1
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2.0k
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Answer: Answer: How to obtain fasta sequences at only mapped sites
2.3 years ago by jkbonfield ★ 1.3k
0
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0
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1.7k
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Comment: Comment: Samtools Error "CIGAR and Query lengths differ" but lengths are the same
2.3 years ago by jkbonfield ★ 1.3k
3
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1
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1.9k
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Answer: Answer: Samtools mean depth and max depth results are discordant
2.4 years ago by jkbonfield ★ 1.3k
0
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0
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2.7k
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Comment: Comment: Error in indexing .bam files from STAR alignment using SAMtools
2.4 years ago by jkbonfield ★ 1.3k
1
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2
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2.1k
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Answer: Answer: Samtools merge/ "The File BAM exists" warning
2.4 years ago by jkbonfield ★ 1.3k
3
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0
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1.7k
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Comment: Comment: How to automate bwa, samtools, bcftools upto variant calling steps without savin
2.7 years ago by jkbonfield ★ 1.3k
108 results • Page 1 of 3
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