the usage of convert2bed

[yueli]

Hi,

Anyone has used the convert2bed?

I got confusing about how to use it. My input file is 1.sam, output file is 1.bed.


Thanks a lot!

Li






li@li-Lenovo:~$ convert2bed -i 1.sam > 1.bed
convert2bed
version: 2.4.12
author: Alex Reynolds

Usage:

$ convert2bed --input=fmt [--output=fmt] [options] < input > output

Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF
and WIG genomic formats to BED or BEDOPS Starch (compressed BED)

[sarvidsson]

The --input (or -i) argument is the format, not the actual input file. It expects input on stdin, which you can pass by using the "<" operator.

[yueluo]

As the Usage is trying to tell you... You need to add the following flags to your command:
--input=bam --output=bed
Also, convert2bed reads/writes through stdin and stdout, which in your case means:
< 1.sam > 1.bed

[yueli]

Thanks, sarvidsson and yueluo.

I got the right answer.

convert2bed -i SAM < 1.sam > 1.bed

[AlexReynolds]

I also include convenience wrapper scripts with BEDOPS, so that you can do:

$ sam2bed < 1.sam > 1.bed
$ sam2starch < 1.sam > 1.starch

Similar wrapper scripts are available for other formats supported by convert2bed (BAM, GFF, GVF, PSL, WIG, etc.).