统计测序深度和覆盖度的工具

1.GATK DepthOfCoverage

cat test.sh 

#!/usr/bin/bash
HG38=/path/hg38/hg38.fa
GATK=/path/biosoft/gatk3.7/GenomeAnalysisTK.jar

java -jar -Xmx10g $GATK  -T DepthOfCoverage \
-R $HG38 \
-o ./test \
-I /path2bam/03_bam_processing/03_base_recal/test.sorted_MarkDuplicates_BQSR.bam \
-L /path2bed/target.bed \
--omitDepthOutputAtEachBase --omitIntervalStatistics \
-ct 1 -ct 5 -ct 10 -ct 20 -ct 30 -ct 50 -ct 100

结果生成四个文件

 4096 Jan 13 21:39 ./
 4096 Jan 13 21:05 ../
 6417 Jan 13 21:39 test.sample_cumulative_coverage_counts
 GenekVIP 6412 Jan 13 21:39 test.sample_cumulative_coverage_proportions
 9362 Jan 13 21:39 test.sample_statistics
 291 Jan 13 21:39 test.sample_summary

　less test.sample_sumary 结果不是很好

sample_id       total   mean    granular_third_quartile granular_median granular_first_quartile %_bases_above_1 %_bases_above_5 %_bases_above_10        %_bases_above_20        %_bases_above_3
test    2025198 17.50   1       1       1       5.1     2.7     2.6     2.5     2.5     2.4     2.3
Total