Annotation for human genomic variation during the BMP4-induced conversion from embryonic stem cells to trophoblast by bone

Whole genomic data of three cell lines were sequenced. These three cell lines are two hESC lines (H1 & H9) by invasion assays and iPSC cell line MRucR. These three cell lines are two hESC lines (H1 & H9) by invasion assays and iPSC cell line MRucR. Paired-end DNA libraries were prepared according to manufacturer’s instructions (Illumina Truseq Library Construction). And then, valid sequencing data is mapped to the reference genome (UCSC hg19) by Burrows-Wheeler Aligner (BWA) software. Reads that aligned to genomic regions were collected for mutation identification and subsequent analysis. Samtools mpileup and bcftools are used to do variant calling and identify SNP, indels. Control-free (Boeva V et al.2012) is utilized to do CNV detection. And BreakDancer (Chen K et al.2009) is applied to detect SV information. And, Single nucleotide variant (SNV) and small somatic insertions and deletions (indels) were identified using Strelka2.