Sample-identity-CHECK

Crosscheck sample swaps

An example shows the relative likelihood of shared (in green) or distinct (in purple) genetic fingerprints across the time-course RNA-seq samples from different individuls. Eight individuals as defined (yellow squares) contain unmatched samples. [LOD: log-odds ratio as described by Javed N. et al. here.; A positive LOD score suggests two samples are more likely derived from the same individul.]

1. Download pre-compiled haplotype maps for hg19 or hg38. see details here

2. Add Readgroups (RGs) for each RNA-seq sample (aligned * deduplicated bam file) for pairwise comparisons

java -Xmx8g -jar \
picard.jar AddOrReplaceReadGroups \
INPUT=Deduplicated.bam/${SAMPLE_NAME}.dedup.bam \
OUTPUT=Deduplicated.bam/${SAMPLE_NAME}.dedup_RG.bam \
RGID=$SAMPLE_NAME \
RGLB=RNAseq \
RGPL=illumina \
RGPU=$SAMPLE_NAME \
RGSM=$SAMPLE_NAME

3. Collect fingerprints (LD blocks information derived from the RNA-seq reads) and run CrosscheckFingerprints.sh

see details here

the "MATRIX_OUTPUT" file could then be used for results visualization re CrossCheck.R

# merge the bam files
samtools merge -@ 12 Merged_RG.bam \
Deduplicated.bam/*.dedup_RG.bam 
# run CrosscheckFingerprints. change the maximum Java heap size if needed.
java -Xmx8g -jar /apps/well/picard-tools/2.21.1/picard.jar CrosscheckFingerprints \
INPUT=Merged_RG.bam \
HAPLOTYPE_MAP=hg38_chr.map \
NUM_THREADS=4 \
OUTPUT=sample.140.crosscheck_metrics.txt \
MATRIX_OUTPUT=sample.140.crosscheck_LOD_Matrix.txt

see example Rescomp runs 2.add.ReadGroups.sh and 3.CrosscheckFingerprints.sh

see example output test_LOD_Matrix_MAPQ255.txt and CrossCheck.R for plotting