Samtools Samtools Statistics & Issues

 

Issue TitleStateCommentsCreated DateUpdated DateClosed Datesamtools 1.10 csi vs 1.13 generation/reading
closed
22021-11-012021-10-272021-11-03mpileup: –output-BP-5 switches output column 7 and 8
open

22021-11-012021-10-27-ampliconclip bug when hardclipping odd-length sequences from the left
closed

12021-10-232021-10-272021-11-03Feature Request: Flag in ampliconclip to clip out everything except target sequence
open

22021-10-222021-10-27-samtools markdup slow in docker
open

22021-10-212021-10-27-idxstats showing extemely large values of chr21 and reduced chrM
closed

22021-10-072021-11-042021-11-02UMI support in markdup
open

12021-10-062021-10-27-filter expression fails with ‘unrecognized flag string’ error
closed

12021-10-052021-10-272021-10-06Multiple threads support for rmdup command?
closed

32021-10-042021-10-272021-10-05samtools tview for protein ncbi-blast blastp output
closed

82021-09-282021-10-272021-09-29How can I get the bining coverage depth using samtools depth?
closed

12021-09-262021-10-272021-10-05samtools coverage doc
closed

12021-09-222021-10-272021-10-19samtools sort can not create a temp file while –write-index and out.bam##idx##out.bam.bai is used
closed

02021-09-212021-10-272021-10-06samtools flagstats : duplication rate
closed

22021-09-172021-10-272021-09-27sorting PacBio bam by name might not be well supported.
open

12021-09-142021-10-27-samtools view problem
closed

52021-09-142021-10-272021-09-14markdup mode for ancient DNA
open

22021-09-132021-10-27-tview: Catalog of loci
open

02021-09-072021-10-27-Whether samtools can select a certain number of cells from the BED file
closed

12021-09-042021-10-272021-09-21samtools merge CRAM output
closed

22021-09-022021-10-272021-09-07Samtools view with regions argument outputs a different number of sequences when outputting to stdout or to file
closed

22021-09-022021-10-272021-09-14Reheader Causes htsjdk Errors if Index isn’t Regenerated
closed

22021-09-012021-10-272021-09-22Anonymous s3 bucket access
closed

32021-08-312021-11-042021-09-23stats -I core dumps
closed

02021-08-312021-10-272021-09-09NotImplementedError:
closed

22021-08-282021-10-272021-08-30samtools markdup – unexpected odd value in count of paired reads in metrics
closed

12021-08-262021-10-272021-08-27Library Support
closed

122021-08-172021-10-272021-08-19Base positions on reads mapped in reverse strand in the pileup format
closed

32021-08-142021-10-272021-08-31samtools stat -p -t 12_3reads.bed fails on i686
closed

52021-08-092021-10-272021-08-09CG tag in BAM/CRAM output?
closed

62021-08-092021-10-272021-08-09Exclude alignments based on presence of tag (regardless of value)
closed

52021-08-052021-10-272021-08-18Erroneous “CRAM CIGAR extends beyond slice reference extents”
closed

12021-07-302021-10-272021-08-05“Incomplete aux field” error in samtools sort with version 1.11.0 but not in 1.9
closed

72021-07-232021-10-272021-08-04Detail information of samtools depth
closed

22021-07-232021-10-272021-07-23Add option “-g” to samtools view to keep reads with *any* of the specified bitflags
closed

42021-07-222021-10-272021-10-06add option to samtools view to unmap aligned reads rather than remove them
closed

52021-07-222021-10-272021-10-07phred scores of deletions
closed

22021-07-152021-11-042021-07-15samtools import: confusing warnings with *.fq.gz inputs.
closed

132021-07-132021-10-272021-08-17samtools coverage fails to parse the regions
closed

22021-07-012021-10-272021-07-06Running samtools view on bam affects the number of variants called by both haplotypecaller and deepvariant
closed

32021-06-292021-10-272021-07-01samtools coverage get different numreads by designated chromosome?
open

42021-06-272021-10-27-Write records that failed to pass the filter into file
closed

12021-06-192021-10-272021-07-06samtools 1.12 view –output-fmt-option filter not work
closed

12021-06-182021-10-272021-06-18samtools v1.12 exclude chromosome chunks when extracting entire chromosomes
closed

22021-06-162021-10-272021-06-22Add option to set output compression level in samtools cat
open

02021-06-162021-10-27-Error using samtools with subjunc bam output [samtools sort: truncated file]
closed

92021-06-112021-10-272021-06-16`–input-fmt-option` filter not work on unmapped reads
closed

72021-06-112021-10-272021-06-11How RNA editing on the genomic forward/reverse (reference) strand is represented?
closed

22021-06-102021-10-272021-08-03Typo in samtools coverage help
closed

12021-06-102021-10-272021-06-22samtools hangs when using a named pipe
closed

42021-05-272021-10-272021-05-27

 

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