BED annotation when start = 0 and chr10 & 20

[jomoxi]

Dear

Thanks for this great piece of work
I've an issue to report: when you try to annotate a BED file, it gets crazy results when start = 0 and chromosome ends with 0 (chr10, 20)

For example, this is the input BED

chr1	0	1000	DEL	SAMPLE_A
chr2	2	2000	DUP	SAMPLE_A
chr10	0	1000	DUP	SAMPLE_A
chr10	1	1000	DEL	SAMPLE_A
chr11	0	1000	DEL	SAMPLE_A
chr20	0	2000	DEL	SAMPLE_A
chr22	1000	2000	DUP	SAMPLE_A

Then we run annotsv (v3.4.4) as follows:

AnnotSV \
-annotationMode full \
-SVinputFile test.cnv.bed \
-genomeBuild GRCh38 \
-outputDir . \
-outputFile test \
-annotationsDir ANNOTSV/3.4.4/ \
-svtBEDcol 4 \
-samplesidBEDcol 5

The resulting tsv looks like this

AnnotSV_ID	SV_chrom	SV_start	SV_end	SV_length	SV_type
1_1_1000_DEL_1	1	1	1000	-999	DEL
10_1_1000_DUP_1	11	0	1000	999	DUP
10_2_1000_DEL_1	10	2	1000	-998	DEL
11_1_1000_DEL_1	11	1	1000	-999	DEL
2_3_2000_DUP_1	3	2	2000	1997	DUP
20_1_2000_DEL_1	21	0	2000	-1999	DEL
22_1001_2000_DUP_1	22	1001	2000	999	DUP

As you can see, there's is no problem with 0-start position except when the chromosome is 10 or 20. Then it sums +1 to the chromosome number and doesn't update start position to 1. It can result in a big mess..

Many thanks in advance!

[lgmgeo]

So strange. Thank you for the report!

[lgmgeo]

Ok, this is a stupid glitch.
Sorry, our servers are down at the moment. I can't push a new version.

Can you edit the file $ANNOTS/share/tcl/AnnotSV/AnnotSV-write.tcl?
The error is line 57 (in the # Formate "SV_start" section). You need to add the "+1" like this:

set lengthTot [expr {$length_updated_AnnotSV_ID+$length_chrom+1}]

Really sorry for the inconvenience.

[jomoxi]

Thanks for the quick response!

Now it works properly. This is the output:

AnnotSV_ID	SV_chrom	SV_start	SV_end
1_1_1000_DEL_1	1	1	1000
10_1_1000_DUP_1	10	1	1000
10_2_1000_DEL_1	10	2	1000
11_1_1000_DEL_1	11	1	1000
2_3_2000_DUP_1	2	3	2000
20_1_2000_DEL_1	20	1	2000
22_1001_2000_DUP_1	22	1001	2000

Bonnes fêtes!

[lgmgeo]

Great!
Thanks again for the report.

Et bonnes fêtes également ;o)

[lgmgeo]

I just added the fix in the patch_AnnotSV branch.