suhail@suhail-HP-Notebook:~/Desktop/data/FAstq$ samtools sort output.bam -n output.sort [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam]
Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null]
what is the issue with reference file ? i have the following in my directory: suhail@suhail-HP-Notebook:~/Desktop/data/FAstq$ ls hg19.fa output.sam Shilpa_Chandna_R2.fastq Tannu_Chandna_R1.fastq.gz trimmed_Shilpa_Chandna_R2.fastq hg19.sthash Shilpa_Chandna.Annotation.txt Shilpa_Chandna_R2.fastq.gz Tannu_Chandna_R2.fastq.gz unpaired_Shilpa_Chandna_R1.fastq hg19.stidx Shilpa_Chandna_R1.fastq Shilpa_Chandna.vcf Tannu_Chandna.vcf unpaired_Shilpa_Chandna_R2.fastq output.bam Shilpa_Chandna_R1.fastq.gz Tannu_Chandna.Annotation.txt trimmed_Shilpa_Chandna_R1.fastq
i am using samtools-1.5 kindly help !!!!!!!!!!!!!!!1
kindly tell me what should i do with this one is there any issue with samtools
the message is clear:
i think you're using an old manual with a recent version of samtools.
thank u it worked . i thought it is giving error due to refrence genome or improper istallation