Hi,
I have tried to down load and instal SAMTools on my mac to make VCF files from a BAM file I have but it is not working?
What I did:
I tried to follow these instructions here (http://sourceforge.net/apps/mediawik...stall_software)
1) went here and waited for auto download (http://sourceforge.net/projects/bio-...r.bz2/download) as I didn't have "wget" installed
2) Moved it to a convent location
3) Open up terminal (Version 2.2.2 (303))
4) tar -jxf samtools-0.1.18.tar.bz2
5) cd samtools-0.1.18
6) ls gives
UTHORS bam2bcf.c bam_index.c bam_sort.c cut_target.c klist.h misc sam_view.c
COPYING bam2bcf.h bam_lpileup.c bam_stat.c errmod.c knetfile.c phase.c sample.c
ChangeLog bam2bcf_indel.c bam_mate.c bam_tview.c errmod.h knetfile.h razf.c sample.h
INSTALL bam2depth.c bam_md.c bamtk.c examples kprobaln.c razf.h samtools.1
Makefile bam_aux.c bam_pileup.c bcftools faidx.c kprobaln.h razip.c win32
Makefile.mingw bam_cat.c bam_plcmd.c bedidx.c faidx.h kseq.h sam.c
NEWS bam_color.c bam_reheader.c bgzf.c kaln.c ksort.h sam.h
bam.c bam_endian.h bam_rmdup.c bgzf.h kaln.h kstring.c sam_header.c
bam.h bam_import.c bam_rmdupse.c bgzip.c khash.h kstring.h sam_header.h
7) Tried Make but got -bash: make: command not found
8) I installed make when I downloaded xtools to get BEDTools-v2.13.3 working.
9) BEDTools in now not working either!!
Do I have to download the xtools all over again?
I have tried to down load and instal SAMTools on my mac to make VCF files from a BAM file I have but it is not working?
What I did:
I tried to follow these instructions here (http://sourceforge.net/apps/mediawik...stall_software)
1) went here and waited for auto download (http://sourceforge.net/projects/bio-...r.bz2/download) as I didn't have "wget" installed
2) Moved it to a convent location
3) Open up terminal (Version 2.2.2 (303))
4) tar -jxf samtools-0.1.18.tar.bz2
5) cd samtools-0.1.18
6) ls gives
UTHORS bam2bcf.c bam_index.c bam_sort.c cut_target.c klist.h misc sam_view.c
COPYING bam2bcf.h bam_lpileup.c bam_stat.c errmod.c knetfile.c phase.c sample.c
ChangeLog bam2bcf_indel.c bam_mate.c bam_tview.c errmod.h knetfile.h razf.c sample.h
INSTALL bam2depth.c bam_md.c bamtk.c examples kprobaln.c razf.h samtools.1
Makefile bam_aux.c bam_pileup.c bcftools faidx.c kprobaln.h razip.c win32
Makefile.mingw bam_cat.c bam_plcmd.c bedidx.c faidx.h kseq.h sam.c
NEWS bam_color.c bam_reheader.c bgzf.c kaln.c ksort.h sam.h
bam.c bam_endian.h bam_rmdup.c bgzf.h kaln.h kstring.c sam_header.c
bam.h bam_import.c bam_rmdupse.c bgzip.c khash.h kstring.h sam_header.h
7) Tried Make but got -bash: make: command not found
8) I installed make when I downloaded xtools to get BEDTools-v2.13.3 working.
9) BEDTools in now not working either!!
Do I have to download the xtools all over again?
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