Lumpy_filter error and which is the best way to generate the discordant paired-end alignments

[biozzq]

Dear @brentp

Recently, I tried to use smoove to detect CNV using the BAM file generated by BWA-MEM as input. However, lumpy_filter always gave me an error: "Segmentation fault (core dumped)"; thus, I changed to use lumpy tranditional usage. During generating the discordant paired-end alignments, I found that the results from the following two pipelines are very different. In my test, the samblaster just reported 0 discordant read pair, but samtools reported many. (1) samtools view -b -F 1294 sample.bam (2) samtools sort -@ 4 -O SAM -n $bam | samblaster -a -e -d $prefix.disc.sam -s $prefix.split.sam -o /dev/null

Hope you can help me with above problems and looking forward to your reply.

Sincerely, Zheng Zhuqing