No positional argument is defined for the tool in GATK4 with SortSam

Question

[xiaolinchu92]

Dear all, I would like to convert the sam file to bam and then sort by coordinate in GATK4.1.8.1 with SortSam. Conversion and Sorting could be done successfully in samtools but the sort order seems not to be coordinate, which is a requirement for the input file with MarkDuplicates in GATK. Therefore, I tried to do this with SortSam in GATK with the following step:

data/home/chuxl/software/gatk-4.1.8.1/gatk  SortSam  -I AA1_bowtie2.sam  -O AA1_bowtie2.gaktsort.bam   SORT_ORDER=coordinate

It breaks with an error message:

Illegal argument value: Positional arguments were provided ',SORT_ORDER=coordinate}' but no positional argument is defined for this tool.

The input sam file are from bowtie2-2.2.9. Its information is as follows:

• @HD VN:1.0 SO:unsorted @SQ SN:contig1 LN:43047 @RG ID:D18AE822 PL:ILLUMINA SM:AA1 @PG ID:bowtie2 PN:bowtie2 VN:2.2.9 CL:"/data/software/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 --rg-id D18AE822 --rg PL:ILLUMINA --rg SM:AA1 -x /data/home/chuxl/data/AA1/Comvar/ref -S AA1_bowtie2.sam -1 /tmp/482547.inpipe1 -2 /tmp/482547.inpipe2" M04650:224:000000000-C4RGP:1:1101:18970:2222 83 contig1 4530 42 115M = 4396 -249 CTCGCCCCGCTGGGCCTGCACCATGGAGCTATCGGGACAGTCCTGCATGAAGTCAGCCATGTCGGCCTGCATCCAGGTCAGCTTGAACCCGAGGAACTCCATCCAGTCCTCCGCG :+::7:>EAA@FCB=9<c,c,?f8eaee:7f,7eeaf@fc7d&lt;9f9faggfc87fc,<fegggggfafggffgggcggggggggggggggggggggggggggggggggggcccc@ as:i:0="" xn:i:0="" xm:i:0="" xo:i:0="" xg:i:0="" nm:i:0="" md:z:115="" ys:i:-7="" yt:z:cp="" rg:z:d18ae822<="" li="">

I am still a newbie in analyzing NGS data. Could anyone help with this? Thanks!

[Pierre Lindenbaum]

shouldn't it be :

data/home/chuxl/software/gatk-4.1.8.1/gatk  SortSam  I=AA1_bowtie2.sam  O=AA1_bowtie2.gaktsort.bam   SORT_ORDER=coordinate

? see https://gatk.broadinstitute.org/hc/en-us/articles/360036510732-SortSam-Picard-