target sequencing?

[tyyiyi]

Hi, I am using lumpy express to call SVs. I have about 60 samples, which are tumor-normal pairs of human. Their sequencing depth is about 1000X, which is targeted sequencing. I want to know if I can use lumpy express to call SVs on my data. Do I need to add -x to exclude locations other than targeted sequencing? lumpyexpress \ -B tumor.bam,normal.bam \ -S tumor.splitters.bam,normal.splitters.bam \ -D tumor.discordants.bam,normal.discordants.bam \ -x ? \ -o tumor_normal.vcf

[ryanlayer]

Ya, I think that would be a good idea. I don't have much experience with targeted sequencing, but I would suggest you use smoove, our new lumpy wrapper

https://github.com/brentp/smoove

On Wed, Jul 24, 2019 at 3:45 AM tyyiyi notifications@github.com wrote:

Hi, I am using lumpy express to call SVs. I have about 60 samples, which are tumor-normal pairs of human. Their sequencing depth is about 1000X, which is targeted sequencing. I want to know if I can use lumpy express to call SVs on my data. Do I need to add -x to exclude locations other than targeted sequencing? lumpyexpress -B tumor.bam,normal.bam -S tumor.splitters.bam,normal.splitters.bam -D tumor.discordants.bam,normal.discordants.bam -x ? -o tumor_normal.vcf

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[tyyiyi]

Thanks for your answer, according to your suggestion, I used smoove, the following is my order:  $smoove call --outdir $outdir --exclude $exclude --name ${tumor}_${normal} --fasta $ref -p 1 --genotype $bam/$tumor.sorted.bam $bam/$normal .sorted.bam  Java -jar $snpsift filter --file ./09_smoove_vcf/256T_S8_256N_S7-smoove.genotyped.vcf "( isVariant( GEN[0] ) && ( GEN[1].AO == 0 ) )" > $smoovefilter/$fname.filter.vcf

After that, only three of the vcf files in the resulting file were variants, and they were tumors (in situ foci, metastases) at different locations in the same patient, and there was only one locus. One of the results is:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 256T_S8 256N_S7

Chr3 41224322 37 N 63940.1 . SVTYPE=DEL;SVLEN=-606;END=41224928;STRANDS=+-:1117;IMPRECISE;CIPOS=-10,9;CIEND=-9,0;CIPOS95=-1, 1;CIEND95=-9,0;SU=1117;PE=1115;SR=2;PRPOS=0,0,8.96779e-320,7.70019e-272,3.02606e-225,1.17849e-178,9.72623e- 133,4.2887e-87,2.96197e-44,0.201243,0.72741,0.0650894,0.00571743,0.000494763,4.21013e-05,3.53283e-06,2.90951e-07,2.35656e-08,1.88497e-09,1.47906e- 10;PREND=9.88365e-13,1.96492e-11,3.83081e-10,7.30425e-09,1.35935e-07,2.4788e-06,4.40018e-05, 0.000767174,0.0130719,0.218022;AC=1;AN =2 GT: GQ: SQ: GL: DP: RO: AO: QR: QA: RS: AS: ASC: RP: AP: AB 0/1: 200:63940.1: -6540, -146, -3081: 8239: 5280:2958:5279:2957:2914:1079:329:2365:1548:0.36 ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:. Is this a correct structural variant?why?

[ryanlayer]

It’s hard to tell if that is real. The pe depth is very high, but the se depth is not. Try visualizing it in either IGV or our tool called samplot.

On Jul 29, 2019, at 8:17 PM, tyyiyi notifications@github.com wrote:

Thanks for your answer, according to your suggestion, I used smoove, the following is my order: $smoove call --outdir $outdir --exclude $exclude --name ${tumor}_${normal} --fasta $ref -p 1 --genotype $bam/$tumor.sorted.bam $bam/$normal .sorted.bam Java -jar $snpsift filter --file ./09_smoove_vcf/256T_S8_256N_S7-smoove.genotyped.vcf "( isVariant( GEN[0] ) && ( GEN[1].AO == 0 ) )" > $smoovefilter/$fname.filter.vcf

After that, only three of the vcf files in the resulting file were variants, and they were tumors (in situ foci, metastases) at different locations in the same patient, and there was only one locus. One of the results is:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 256T_S8 256N_S7

Chr3 41224322 37 N 63940.1 . SVTYPE=DEL;SVLEN=-606;END=41224928;STRANDS=+-:1117;IMPRECISE;CIPOS=-10,9;CIEND=-9,0;CIPOS95=-1, 1;CIEND95=-9,0;SU=1117;PE=1115;SR=2;PRPOS=0,0,8.96779e-320,7.70019e-272,3.02606e-225,1.17849e-178,9.72623e- 133,4.2887e-87,2.96197e-44,0.201243,0.72741,0.0650894,0.00571743,0.000494763,4.21013e-05,3.53283e-06,2.90951e-07,2.35656e-08,1.88497e-09,1.47906e- 10;PREND=9.88365e-13,1.96492e-11,3.83081e-10,7.30425e-09,1.35935e-07,2.4788e-06,4.40018e-05, 0.000767174,0.0130719,0.218022;AC=1;AN =2 GT: GQ: SQ: GL: DP: RO: AO: QR: QA: RS: AS: ASC: RP: AP: AB 0/1: 200:63940.1: -6540, -146, -3081: 8239: 5280:2958:5279:2957:2914:1079:329:2365:1548:0.36 ./.:.:.:.:.:.:.:.:.:.:.:.:.:.:. Is this a correct structural variant?why?

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[tyyiyi]

Thank you for your suggestion, I will use IGV to visualize it.