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general_preprocessing.log
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INFO:general_preprocessing:
Log File for general preprocessing
INFO:general_preprocessing:command to bgzip file: bgzip -c /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf > /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz
INFO:general_preprocessing:command to tabix file: tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz
INFO:general_preprocessing:file before reheader: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz
INFO:general_preprocessing:file after reheader: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz
INFO:general_preprocessing:command to reheader vcf: echo "UDN771219" | bcftools reheader -s - -o "/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz.tmp" "/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz"
INFO:general_preprocessing:command to tabix file: tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz
INFO:general_preprocessing:file before multiallelic splitting, left allignment and normalization: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz
INFO:general_preprocessing:file after multiallelic splitting, left allignment and normalization: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz
INFO:general_preprocessing:command to do multiallelic splitting, left allignment and normalization:bcftools norm --multiallelics - --check-ref x --fasta-ref=/share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz --output-type z --output /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz
INFO:general_preprocessing:command to tabix file: tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz
INFO:general_preprocessing:file before duplicate removal: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz
INFO:general_preprocessing:file after duplicate removal: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz
INFO:general_preprocessing:command for duplicate removal bcftools norm -d both /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz --output-type z --output /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz
INFO:general_preprocessing:command to tabix file: tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz
INFO:general_preprocessing:file before stripping chr prefix: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz
INFO:general_preprocessing:file after stripping chr prefix: /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz
INFO:general_preprocessing:command for stripping chr prefix bcftools annotate --rename-chrs /scratch/PI/euan/common/udn/code/chromosome_notation.txt /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz --output-type z --output /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz
INFO:general_preprocessing:command to tabix file: tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz
INFO:general_preprocessing:cmd to rename file to the new name: mv /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
INFO:general_preprocessing:command to tabix file: tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz