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202307-FeBY2
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bed
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run_gatk_hsM.pbs

run_gatk_hsM.pbs 1.8 KB
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  1. #PBS -N test
    2. 

  2. #PBS -j oe
    3. 

  3. #PBS -l ncpus=4
    4. 

  4. #PBS -l nodes=1
    5. 

  5. #PBS -l mem=20G
    6. 

  6. #cd ${PBS_O_WORKDIR}
    7. 

  7. bed=$1
    8. 

  8. home=/home/guochangquan
    9. 

  9. gatk=/cgdata/guocq/soft/GATK/4.1.2.0/gatk
    10. 

  10. verify=/cgdata/guocq/soft/verifyBamID_1.1.3/verifyBamID/bin/verifyBamID
    11. 

  11. b37=$home/database/GATK/b37/human_g1k_v37_decoy.fasta
    12. 

  12. b37_dict=$home/database/GATK/b37/human_g1k_v37_decoy.dict
    13. 

  13. idtwes_b37=/cgdata/guocq/script/wes-cnv/xgen-exome-research-panel-probes-b37.bed
    14. 

  14. mby2_b37=/cgdata/guocq/script/MBY2-b37/MBY2_20180802.b37.6.bed
    15. 

  15. bia_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.vcf.gz
    16. 

  16. idtwes_bia_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.IDTWES.vcf.gz
    17. 

  17. mby2_bia_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.MBY2.ip80.vcf.gz
    18. 

  18. thal_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.Thal.ip80.vcf.gz
    19. 

  19. thal_bed_b37=/cgdata/guocq/script/Thal_wf/Thal_bed_20180702.b37.bed
    20. 

  20. 

  21. test -d metrics || mkdir metrics
    22. 

  22. #bed=/cgdata/guocq/script/AZF-b37/190702_AZF.merge.filter-3.b37
    23. 

  23. hg19_dict=/ngs/Bioinf/Database/ref/hg19/seq/hg19.dict
    24. 

  24. shome=/cgdata/guocq/script/AZF-b37
    25. 

  25. #$gatk BaitDesigner \
    26. 

  26. #-T Thal_bed_20180702.b37.interval_list \
    27. 

  27. #-R $b37 --DESIGN_NAME TEST_thal_120 --BAIT_OFFSET 120
    28. 

  28. #exit
    29. 

  29. 

  30. test -f $bed.interval_list || \
    31. 

  31. $gatk BedToIntervalList \
    32. 

  32. -I $bed.bed \
    33. 

  33. -O $bed.interval_list \
    34. 

  34. -SD $b37_dict
    35. 

  35. 

  36. exit
    37. 

  37. 

  38. $gatk CollectHsMetrics \
    39. 

  39. -I $bam_dir/${sample}.bam \
    40. 

  40. -BI $bed.interval_list \
    41. 

  41. -TI $bed.interval_list \
    42. 

  42. -O metrics/${sample}_hs_metrics.txt \
    43. 

  43. -R $b37 \
    44. 

  44. --PER_TARGET_COVERAGE metrics/${sample}_hs_target.txt \
    45. 

  45. --COVERAGE_CAP 6000 -MQ 0 
    46. 

  46. 

  47. cd metrics
    48. 

  48. Rscript $shome/azf_cov_norm.r $shome/AZF_ref_exon_cov-3.xls ${sample} 
    49. 

  49. perl $shome/AZF_dup_norm.pl ${sample}_norm.cov.xls
    50. 

  50. Rscript $shome/azf_seg.r ${sample}
    51. 

  51. perl $shome/AZF_del_type.pl ${sample}
    52.