Dindel - stage 1 error

[N311V]

Hi All,

I'm getting "Error parsing input options. Usage:" message from Dindel.

The bam file and ref fast file are both indexed with samtools.

Here are a few lines of a bam file I'm trying to use. The mapping in this example was done using bwa mem followed by GATK indel realignment.

FCD0RDBACXX:1:1101:11722:138337#TTAACCGG	99	scaffold1.1|size6200209	1	40	20S80M	=	370	469	AAATTCTTATCTTTTGGTAGGCCCTACCTCATTTTATAGCTTATTGCTATTTTTTTTCGTTGCGACCGTAGAATCGTGTTTGTATACCCTTGCAGGGGAT	@@CFFFFFHHHHHIGIICHHGGHGCGHIJJIJJJJJIBGIJJJIJIJCCIGIGGGIIGGCFGHFFDCD;?B5>CC??A??CC?CD>3:>>CC>:ABD&59	MD:Z:77T2	RG:Z:sample34_wildtype	NM:i:1	MQ:i:60	AS:i:77	XS:i:84
FCD0RDBACXX:1:1305:5555:141592#TTAACCGG	99	scaffold1.1|size6200209	1	50	8S92M	=	359	458	TTTGGTAGGCCCTACCTCATTTTATAGCTTATTGCTATTTTTTTTCGTTGCGACCGTAGAATCGTGTTTGTATACCCTTGCAGGGTATTATTATTTCAGT	CCCFFFFFHGHHHIIIJJGHGIJGIDHIIIDHIDDGGIIJJJJJJJJHGGGGGEECBDDDDDDDDB?BDCDDEEDCCDD<>C>BB3?ADDDEEEEEEDDE	XA:Z:scaffold1.1|size6200209,+5871,37M1I62M,2;	MD:Z:92	RG:Z:sample34_wildtype	NM:i:0	MQ:i:60	AS:i:92	XS:i:87
FCD0RDBACXX:1:1101:9554:185422#TTAACCGG	163	scaffold1.1|size6200209	5	60	100M	=	389	484	TACCTCATTTTATAGCTTATTGCTATTTTTTTTCGTTGCGACCGTAGAATCGTGTTTGTATACCCTTGCAGGGTATTATTATTTCAGTCAGAAGTTTGCA	C@BFFFFFHHHHHJJJIJJIGGIGGIIJJJJIJIJHIGGIIGJI@ACAEH?B?DBCEDBDDDCDDCDDDCDDD9?CDEDEDEEDD@CDDDDDCDACDA@A	XA:Z:scaffold1.1|size6200209,+5883,25M1I74M,1;	MD:Z:100	RG:Z:sample34_wildtype	NM:i:0	MQ:i:60	AS:i:100	XS:i:92

Here is an example of the fasta ref format.

>scaffold1.1|size6200209
GCCCTACCTCATTTTATAGCTTATTGCTATTTTTTTTCGTTGCGACCGTAGAATCGTGTTTGTATACCCTTGCAGG

And here is the command.

dindel --analysis getCIGARindels \
 --region 648000-652000 \
 --tid scaffold59.1\|size703044 \
 --bamFILE file.bam \
 --outputFile file.dindel_output \
 --ref scaffolds.fa

Any help would be appreciated.

Thanks