SvABA refilter does not support -Y and -B?

[chunyangbao]

Hi,

When I used SvABA refilter, I got the following ERROR message. It seems that SvABA refilter does not support -Y and -B. Do you have similar experience? The FH Version of my SvABA is 134.

$ svaba refilter -i sample.bps.txt.gz \ -b sample.contigs.bam \ -a ./refilter/sample \ -g Homo_sapiens_assembly19.fasta \ -D data.broadinstitute.org/snowman/dbsnp_indel.vcf \ -Y data.broadinstitute.org/snowman/viral_database/viral.1.1.genomic_ns.fna \ -B data.broadinstitute.org/snowman/hg19.svaba.exclude.bed

refilter: invalid option -- 'Y' refilter: invalid option -- 'B'

Then, I tried install the newest SvABA to fix above issue. But, I got the following ERROR messages. Could you please help me to figure out? Your help is much appreciated!

cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory

use .git-2.5.0 use .curl-7.47.1 use .gcc-5.2.0 use .zlib-1.2.8

Thanks, Chunyang DFCI

[walaj]

Hi Chunyang,

There have been some fixes so I agree it would be good to re-install. It seems you are missing the bzip2 library, so I would try: use .bzip2-1.0.6. Doing a use Samtools may also do the trick.

Regarding Y and B for refilter -- since the variants are flagged as either in a blacklist region (B) or as belonging to a microbial genome (Y) during the original run, I don't allow them as parameters in refilter. The idea of refilter is to set a different cutoff for the LOD scores, but changing B or Y would change how the original calls were generated.

However, I see that the help section for refilter says these are parameters. This is incorrect and I just pushed a change to fix this.

(BTW, I'm thinking I may deprecate "refilter" because the unfiltered VCF already contains all the variants, and so one could filter that using any number of pre-existing VCF parsing / filtering tools (e.g. vcftools). That's probably a better workflow than trying to support my own VCF filtering pipeline.)

Hope that helps, Jeremiah

[chunyangbao]

Very clear. Thank you!

From: Jeremiah Wala notifications@github.com Sent: Wednesday, March 13, 2019 4:12 PM To: walaj/svaba svaba@noreply.github.com Cc: Bao, Chunyang Chunyang_Bao@DFCI.HARVARD.EDU; Author author@noreply.github.com Subject: Re: [walaj/svaba] SvABA refilter does not support -Y and -B? (#55)

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Hi Chunyang,

There have been some fixes so I agree it would be good to re-install. It seems you are missing the bzip2 library, so I would try: use .bzip2-1.0.6. Doing a use Samtools may also do the trick.

Regarding Y and B for refilter -- since the variants are flagged as either in a blacklist region (B) or as belonging to a microbial genome (Y) during the original run, I don't allow them as parameters in refilter. The idea of refilter is to set a different cutoff for the LOD scores, but changing B or Y would change how the original calls were generated.

However, I see that the help section for refilter says these are parameters. This is incorrect and I just pushed a change to fix this.

(BTW, I'm thinking I may deprecate "refilter" because the unfiltered VCF already contains all the variants, and so one could filter that using any number of pre-existing VCF parsing / filtering tools (e.g. vcftools). That's probably a better workflow than trying to support my own VCF filtering pipeline.)

Hope that helps, Jeremiah

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