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Seek for help running representation unifcation #121
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RU doesn't require |
The result of my running is as follows, can you help me to see what is wrong? This is WhatsHap 1.2.1 running under Python 3.6.10 == SUMMARY == == SUMMARY == |
The command I execute is as follows Setup variablesCLAIR3="/work/Clair3-main/clair3.py" # clair3.py Input parametersPLATFORM="ont" # e.g. {ont, hifi, ilmn} Chromosome prefix ("chr" if chromosome names have the "chr" prefix)染色体前缀CHR_PREFIX="chr" array of chromosomes (do not include "chr"-prefix)CHR=(22) Number of threads to be usedTHREADS=24 The number of chucks to be divided into for parallel processing#并行加工需分割的卡盘数量 Minimum AF required for a candidate variantMIN_AF=0.08 Temporary working directorySPLIT_BED_PATH="${OUTPUT_DIR}/split_beds" mkdir -p ${SPLIT_BED_PATH} 2. Phase VCF file using WhatsHapTo apply representation unification, using a phased read alignment is highly recommended in order to get more precious unified result.WhatsHap phasing vcf file if vcf file includes '|' in INFO tagcd ${OUTPUT_DIR} WhatsHap phasing vcf file if vcf file includes '|' in INFO tag${WHATSHAP} unphase ${VCF_FILE_PATH} > ${OUTPUT_DIR}/INPUT.vcf.gz WhatsHap phase vcf file${PARALLEL} --joblog ${PHASE_VCF_PATH}/phase.log -j${THREADS} Index phased vcf file${PARALLEL} -j ${THREADS} tabix -p vcf ${PHASE_VCF_PATH}/phased_{1}.vcf.gz ::: ${CHR[@]} ```#3. Haplotag read alignment using WhatsHap WhatsHap haplotags bam file${PARALLEL} --joblog ${PHASE_BAM_PATH}/haplotag.log -j${THREADS} Index the phased bam file using samtools${PARALLEL} --joblog ${PHASE_BAM_PATH}/index.log -j ${THREADS} ${SAMTOOLS} index -@12 ${PHASE_BAM_PATH}/{1}.bam ::: ${CHR[@]} Split bed file regions according to the contig name and extend bed region${PARALLEL} --joblog ${SPLIT_BED_PATH}/split_extend_bed.log -j${THREADS} #Get true variant label information from VCF file #5. Unify Representation for true variant set and candidate sites #6. Merge and sort unified VCF output |
Still no hint for the empty output. Could you check each file's validity in step 5? We speculated that some files are empty or missing in your step 5. |
After I reinstalled the environment, it can run correctly, I think it should be an environment problem. |
libclair3 is built via this command( |
Hi,
I met a problem in the step of representation unification.
After I execute the command according to representation_unification.md, my vcf output folder is empty. I carefully check the steps and find that the CreateTensorFullAlignment command is missing in step 4 in the representation_unification.md file provided now, but after I add this command Found that the files in my CANDIDATE_DETAILS_PATH are all empty. Can you help me?
Sincerely
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