glactools
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grenaud
command-line tools for the management of genotype likelihoods and allele counts
Hi, I've been using glactools for a while now, with no issues, to manipulate files and export them to treemix format. Today I was working on a new sheep dataset...
hello, grenaud! now, I just have an outgroup vcf file (other mammals not human), could you tell me how can I transform vcf file to epo file?
Hello. I have a problem using vcfm2acf. glactools vcfm2acf --onlyGT --fai human_g1k_v37.fasta.fai chr1.recode.vcf > chr1.acf.gz **error message** libgab.h base2int() Invalid base * Please let me know if any improvements can...
hello, i want to install this software,but i meet this question as follows,please help me to solved its. bam_ampliconclip.c: In function ‘amplicon_clip_main’: bam_ampliconclip.c:639:23: warning: ‘sites’ may be used uninitialized in...
Hi, I want to know whether bam2acf only accepts one bam file as input, how about multiple samples bam files of a population, how to deal with this?
Hi, I used glactools to convert multiple sample vcf file to acf format. However, a problem has occured as follows: ``` (base) [shali@vm-login02 test]$ glactools vcfm2acf --onlyGT --fai /public/home/fan_lab/shali/reference/hg38.fa.fai chr22.vcf.gz...
Hi, I have a multi-samples VCF that I would like to convert to G-Phocs input format. Is there a way to accomplish this task in glactools? Thank you!
Hi I Need Convert plink(bed-bim-fam) to treemix input With This Command: glactools bplink2acf --fai human_g1k_v37.fasta.fai afghan | glactools acf2treemix - | gzip > treemix.gz but error: Cannot write to /dev/stdout...
Hi, Thanks for the grear program. It looks like I cannot use bed track with glactools bam2acf: $ glactools bam2acf --bed $bed $ref_fa $bam test | glactools view - |...
hi,when I installed glactools,I met a problem like that,can you give me some advise. Thank you very much. ReadTabix.cpp:(.text+0x1a8): undefined reference to `Tabix::setRegion(std::__cxx11::basic_string&)' lib/libglactools.a(ReadTabix.o): In function `ReadTabix::readLine(std::__cxx11::basic_string&)': ReadTabix.cpp:(.text+0x20d): undefined reference...
