NGS talks

Whole-Exome Sequencing to Identify Somatic Variants in Cancer - Yardena Samuels(from NHGRI)

Next Generation Sequencing

Determine genetic map position of SNP':
online tool
Conway Institute Bioinformatics Service

An overview of NGS technology and platforms:
http://www.seqwright.com

Blog on NGS technology (www.yuzuki.org) by Dale Yuzuki:

Next Generation Technologist 

How to remove duplicates reads using picard:

java -Xmx2g -jar /usr/local/picard-tools/MarkDuplicates.jar 
                            MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000
                            METRICS_FILE=out.metrics 
                            REMOVE_DUPLICATES=true 
                            ASSUME_SORTED=true  
                            VALIDATION_STRINGENCY=LENIENT 
                            INPUT=input.sorted.bam 
                            OUTPUT=out.dedup.bam 

BAM file reheader trick (that works):

java -jar /home/zhengyuan/picard-tools-1.105/AddOrReplaceReadGroups.jar \

I=test.srt.bam O=test.srt.rhd.bam LB=wzy PL=illumina PU=wzy SM=wzy

samtools index  test.srt.rhd.bam

Then you can proceed for others tasks like GATK coverage analysis.