jxcao98

Hello, I have applied manta on a mark duplicated BAM, but overlap SVs within the same sample were reported, like this: SV1: `1 14436308 MantaDEL:1023:0:1:1:0:0 N 999 Ploidy SVTYPE=DEL;SVLEN=-1933;END=14438241;CIPOS=0,0;CIEND=0,0;PRPOS=1.0;PREND=1.0;STRANDS=+-:44;SU=44;PE=32;SR=12;CIPOS95=0,0;CIEND95=0,0 GT:FT:GQ:PL:PR:SR...

Hi, Thanks for your wonderful tool. I plan to perform joint-calling on 1300 individuals (30X WGS) following the Manta + Svimmer + Graphtyper pipeline. I have run the Manta for...

Can't exec "samtools"

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Hi Thanks for your nice tool! I tried to run VEP by Singularity, but I got confused about where the path of Samtools should be placed. I have added the...

How to handle incompletely resolved insertion sequences in short-read sequencing for compatibility with PART

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郑博士您好， 感谢您开发的好工具！ 因为PAnpop Realign and Thin工具对输入的VCF格式有要求，即必须在REF和ALT字段提供具体序列。对于二代测序，DEL/DUP应该不是问题，但是INS往往难以完全解析。以常见的Manta工具为例，它可能只能解决断点周围的插入序列，导致我们无法为INS填充正确的ALT字段。 请问您对此有何建议？是否对于二代测序的结果合并，我们必须忽略大多数难以解析的INS？ 谢谢！