获取 GATK 参数错误并且不明白？

Question

你好 bash 程序员，我正在使用 GATK 并尝试遍历我的 bam 文件并使用我的 target_intervals 和已知的插入缺失进行本地重新对齐。下面是我正在尝试的代码。我希望有人可以帮助解决错误并更正我的代码。

# do the local realignment.
echo "local realignment..."

for file in `ls -d adp/map/*marked_duplicates.bam`
do
java -jar ~/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R ~/flybase/fb-r5.57/dmel-all-chromosome-r5.57.fasta \
-I $file \
-known adp/map/*indel_intervals.vcf \
-targetIntervals adp/map/*target_intervals.list \
-o ${file}_realigned_reads.bam
done

wait

# Create a new index file.
echo "indexing the realigned bam file..."

for file in `ls -d adp/map/*realigned_reads.bam`
do
~/software/samtools-1.2/samtools index $file
done

错误：查找时，这似乎是一个编码问题，但我没有看到。

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid argument value 'adp/map/360M_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 10.
##### ERROR Invalid argument value 'adp/map/517_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 11.
##### ERROR Invalid argument value 'adp/map/517M_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 12.
##### ERROR Invalid argument value 'adp/map/900_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 13.
##### ERROR Invalid argument value 'adp/map/900M_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 14

.

Answer 1

至少部分问题是您命令中的 *。 GATK 不能很好地处理 glob。要为一个参数指定多个值，请多次指定该参数。

即而不是

-known adp/map/*indel_intervals.vcf

您需要用单独的参数指定每个文件

-known adp/map/first_file.indel_intervals.vcf
-known adp/map/second_file.indel_intervals.vcf

可能还有其他问题。例如，我不确定 -targetIntervals 是否可以将多个文件作为输入。另外，那是非常旧的 gatk 版本，您可能需要升级到 3.8。

获取 GATK 参数错误并且不明白？

Getting GATK argument error and dont understand?

bash

alignment

sequence

dna-sequence

gatk