output N for REF column

[brentp]

IGV errors on variants with "." for the REF but does fine with "N"

[qinx2016]

I use lumpyexpress, but the column of REF show "N" not "A/T/G/C" in the result vcf file. How to reslove it? vv

[i19870503]

But how could I get the sv sequence from the vcf result file ?

[ryanlayer]

On Nov 29, 2017, at 3:54 AM, Zhongliang [email protected] wrote:

But how could I get the sv sequence from the vcf result file ?

You can use the POS and END coordinates to pull the sequence from your regency file.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[i19870503]

OK, thanks. But speedsed for bacteria make me confused on the results, for example NC_007795.1 10 246 N <DUP> . . SVTYPE=DUP;STRANDS=-+:1309;SVLEN=2821351;END=2821361;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=1309;PE=656;SR=653 GT:SU:PE:SR ./.:759:381:378 ./.:550:275:275 The length of sv is almost the full length of the genome, is there anything wrong when run the program?

[ryanlayer]

Is this because the genome is circular?

On Thu, Nov 30, 2017 at 1:26 AM, Zhongliang [email protected] wrote:

OK, thanks. But speedsed for bacteria make me confused on the results, for example NC_007795.1 10 246 N <DUP> . . SVTYPE=DUP;STRANDS=-+:1309; SVLEN=2821351;END=2821361;CIPOS=0,0;CIEND=0,0;CIPOS95=0, 0;CIEND95=0,0;SU=1309;PE=656;SR=653 GT:SU:PE:SR ./.:759:381:378 ./.:550:275:275 The length of sv is almost the full length of the genome, is there anything wrong when run the program?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/arq5x/lumpy-sv/issues/183#issuecomment-348116505, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUdGwu97Vb9L8CFOG43MY7J14fv2bks5s7maigaJpZM4M0eV7 .

-- Ryan Layer

[jammywwh]

I use lumpyexpress, but the column of REF show "N" not "A/T/G/C" in the result vcf file. How to reslove it? vv

same issue，can anyone help us?