An efficient pipeline for sequence based variant detection in comercial chicken lines

M.Gholami, M.Siedel, G.Haberer, T.Strom, R. Preisinger, H. Simianer.

Within the Synbreed project one of the primary aims is the resequencing of European maize, chicken and cattle genotypes using conventional next generation sequencing technologies. Our project (which is a subproject of Synbreed) involves resequencing and variant calling in chicken. Currently three individuals of commercial egg-laying chicken (white leghorn) have been sequenced using the paired-End Illumina sequenig technology with an average 30x coverage. With the availability of the new fully sequenced chicken genome and the three individuals' sequences, we established a reliable pipeline for realignment and variant calling in chicken. We used diffrent aligning and variant calling software for this purpose such as stampy in hybrid with BWA, samtools and vcfutils. Two separate groups have done the aligning and variant calling in these three sequenced chicken, simultaneously, with a slightly diffrent pipeline. In total 4.7 to 5 million variants with an average quality of 150 have been detected, with 3.7 and 1.1 million homozygous and heterozygous variants, respectably. 80% of the unfiltered variants are common within the three individuals. Approximately 4.5 million SNP's and 0.5 million indels have been discovered, which are now in the validation and filtering process.